Flynn is just the tip of a large and dark iceberg
An iceberg that threatens the ship of state. I think it must be obvious even to Trump’s followers that Flynn is just a symptom of a much larger problem. Trump picked Flynn, and Flynn is the third of Trump’s close associate that has had to resign because of close relations with Russia: Carter Page and Paul Manafort are the other two.
Trump is picking these men. That’s not good: he doesn’t know how to pick men (though, of course, there’s the interesting possibility that they were picked for him).
And worse: Trump knew all about this Flynn incident for weeks. His administration has said exactly that: we knew about it and we’ve been “working on it” for weeks. Fortunately all that work was able to completed within 24 hours of the Washington Post publishing the story. Coincidence? You be the judge.
The thing is, all of the above is public knowledge: widely reported and well known. So surely some of the Trump supporters must be starting to get a little uncomfortable. These are not subtle things. These are plain bald facts.
More to the point, will the GOP in Congress do anything?
Well, Trump is clearly very thin-skinned and quick to take offense, and when it happens he is extremely vindictive and impulsive. So I imagine their fear is simply much stronger than adherence to their principles (which has always been pretty loose: look at Jason Chaffetz for a great example, a “before-and-after” right in himself, all bark-and-growl at Hillary Clinton, lining up investigations for years to come, but quiet as a mouse with Trump—Chaffetz has more or less explicitly said that he will do nothing to investigate Trump) or to the Constitution. Plus they stand to make a lot of money if they go along because Trump has opened the lobbyist floodgate and by his very example has said, loud and clear, “Conflicts of interest are OK!” Kickbacks are okay now!
Those are pretty strong forces, much stronger (as it turns out) than the Republicans in Congress.