Since the Pentagon's boarding party landed in the White House, the focus of foreign affairs has shifted away from what Trump and the Trump movement held to be the greatest national security threat -- "radical, Islamic, terrorism" -- and right back to the out-of-date Cold War obsession with countering Russia and anyone who eluded our sphere of influence back then.
The brass at the Pentagon and Deep State broadly intends to continue the failed policies of the "Axis of Evil" framework, which sought to update the Cold War geopolitical positioning for an era where there was no more Soviet Union and Communism was in steep decline worldwide. For the new millennium, the anti-Communist rhetoric was dropped and now the narrative was all about evil dictators who are trying to acquire weapons of mass destruction that they might use on their own people, and after that, on ours. Therefore, we must intervene and do regime change and/or building democracy afterward, to bring to power other leaders who are not evil dictators intent on getting WMD to use at their whim.
This vision would be laughable if it had not led to the utter disaster of the Iraq War, not to mention our toppling of Qaddafi in Libya. Neither of those countries has come under the US sphere of influence, and none of the material wealth there (oil) is flowing into our hands either. And now that the dictators are gone, the Islamic terrorists who they'd been keeping in check are now free to terrorize their own neck of the world, and the West as well.
Trump tried to emphasize this craziness during the campaign, by pointing out how these dictators may have been "bad guys" but at least they were keeping radical Islamic terrorists from running amok. Left with only those two options, the choice is obvious, yet our military Establishment has repeatedly chosen to topple dictators despite the outcome of spreading jihadism.
Take a look at the nations targeted by the Cold War, Axis of Evil, War on Terror framework -- Cuba, North Korea, Libya, Syria, Iraq, and Iran. Five of those six were ruled by explicitly secular or even atheist governments, excepting Iran.* Their crime for which they are to be punished is not agreeing to fall under the US sphere of influence, it's as simple as that. With the waning of Castro influence in Cuba, maybe the neo-Cold Warriors will focus on Venezuela instead.
The Bush administration went to pains to make clear that they had no beef with Islam, and that the al-Qaeda types were hijacking an otherwise peaceful religion, etc. Bush apologized for describing the War on Terror as a "crusade," i.e. for introducing a religious tone. The Bush people never railed against Islam, Islamism, Islamists, Islamic terrorism, radical Islam, radical Islamic terrorism, or any conceivable way of referring to jihad and jihadists.
And why would they? Aside from Iran, their enemies were secular or atheist rulers who were actively suppressing radical Islam. And our key allies in the region, especially Saudi Arabia, Turkey, and Pakistan, are either favorable toward or are enthusiastic participants in radical Islam -- and in spreading it far and wide. Our NATO allies, especially Turkey but including Western Europe, are letting jihadism incubate within their borders, and support jihadism via support for the Saudis. But they're opposed to Russia, so NATO is just A-OK with the Pentagon.
That is why the military Deep State will only focus on a particular jihadist ally that goes out of control, or that draws too much negative publicity to itself, such as al-Qaeda and ISIS. As long as the jihadists re-brand themselves, and agree to be allies of the US, the Pentagon prefers them to the secular governments that do not want to be client states of the US.
The last time Trump used some variation of "radical Islamic terrorism" on Twitter was February 6, roughly one week before his NSC Advisor Michael Flynn was forced out of the White House by the Pentagon boarding party. It's not as though there haven't been major incidents of Islamic terrorism since then -- the French police officer who was assassinated on April 20, buses full of child evacuees being blown up in Syria, and on and on. Yet nobody in the administration is railing against "radical Islamic terrorism," even to promote a general policy rather than respond to a particular incident.
Trump made such a big stink about Obama, "He won't even use the term, 'radical Islamic terrorism'". He has used that phrase for years and years, and suddenly he stops using it when there's a broader shake-up in his Cabinet that expels one of the few Generals who is skeptical about re-igniting the Cold War, who doesn't think Syria is the enemy (and who actually left open the possibility that the 2013 chemical attack in Syria was a false flag by the jihadists), and who views radical Islam as the #1 threat facing us today.
See here for a review of Flynn's views on radical Islam. Even if you think he's exaggerating somewhat about how deeply ingrained jihadism is to Islam per se (rather than, say, certain groups of Muslims like the Arabians, or certain schools like the Hanbali Sunni), the point remains that he's focused on an actual serious threat rather than a boogeyman like Russia, and that his views would lead him to be more wary of blindly supporting Saudi Arabia, and less wary of partnering with Syria, in solving the problem. That puts him at odds with the military Establishment, but right on the same wavelength as Trump and his supporters, who want to re-align our foreign policy away from the dead Cold War and toward the pressing concerns of radical Islam -- and Muslim mass migration.
Sebastian Gorka is another White House figure who nearly got shoved out by the Establishment for focusing on jihadism rather than secular strongmen who resist US control. Steve Bannon and Stephen Miller fall into this camp as well, although their positions seem safer for now.
Secretary of Defense Mattis is squarely within the "don't criticize Islam" camp, lest it antagonize our loyal Saudi allies who blew us up on September 11th (including the very Pentagon building itself -- some gratitude with those Bedouin). So is Flynn's replacement, McMaster (Mike Cernovich says he's being promoted out, but if his replacement is also part of the Pentagon boarding party, nothing will substantially change).
And Secretary of Homeland Security Kelly said during his confirmation hearings that general surveillance of mosques here should play no role in preventing terrorist attacks -- despite that being common practice in the NYC area after 9/11, helping to foil several plots. Trump ally Rudy Giuliani defended that practice many times during 2016, so why isn't he or someone like him the Secretary? The Pentagon brass would veto such a move, as it would contradict their policy of being as Muslim-friendly as possible, up to letting Salafi clerics radicalize people right here within our borders who will blow us up on our own soil.
Going forward, we will discover how much Trump can push back against the Pentagon Party that sees a Republican in the White House as its carte blanche. Regardless of personnel changes, if their views stay roughly constant, it will show the institutional strength of the Pentagon and the relative weakness of the President and his inner circle -- who, in all fairness, came into Washington with essentially no connections or leverage, other than the electoral victory itself. Trump and his fellow travelers would have to mobilize us in order to flex any muscle against the Pentagon -- whether calling in to our representatives, spreading a social media campaign, holding protests, or what have you.
If foreign policy moves away from Cold War / Axis of Evil obsessions, and back toward the focus on radical Islam from the campaign trail, it will show that the Trump movement is not so beholden to the military faction of Deep State.
After Flynn was sidelined, the Pentagon has had the upper hand, but it is still a fluid situation for now. If it's a year or two years of this crap, then we will have found out that the Pentagon is too powerful to counteract from within the government, and that only a truly catastrophic failure of their own (e.g. provoking Russia into a nuclear war) will discredit their vision, albeit a little too late.
* To the extent that Iran has supported armed rebellions elsewhere (mainly via Hezbollah), it has been for national liberation or anti-imperial purposes, such as getting the Israeli and American militaries out of Lebanon, rather than to convert others to Shia Islam at the barrel of a gun, to genocide non-Shia groups, to destroy buildings and shrines that their sect does not honor, or to otherwise engage in religiously motivated mayhem.