Yesterday, Sally Yates testified that "we believed that General Flynn was compromised." The rest, well, we already knew. He was taking money from Russia, meeting with the Russians, etc., and it took a hell of a long time for Trump to fire Comrade Flynn. For all of the "Trump is a Russian stooge" hypotheses floating around, let's review all of the possibilities remaining:
1) Yup, Trump could be a Russian stooge. The "dossier" (or at least, the non-salacious parts) have a reasonable possibility of being true, and we know that Russia tries to get blackmail material on everyone. Remember that all they would need to blackmail Trump is to get their hands on some of his more interesting tax returns. Combine that with his natural affinity for Putin, and hey, what are a few cruise missiles between friends? If that's what's going on, Trump would be fine with Flynn around because they'd be in the same boat.
2) Trump ignored the warnings because he just has a personal affinity for batshit crazy conspiracy theorists, which is what Flynn is. Trump isn't what you would call an "evidence" kind of guy. Show him evidence that Flynn was being controlled by Russia and he wouldn't really care, as long as Flynn spouted some really out-there shit about Obama, muslims, chem-trails, vaccines and, hell, let's throw in Slenderman.
3) Trump ignored the warnings because he discounted the messengers. It wasn't just Yates, but Obama personally who told the guy that Flynn couldn't be trusted, making it extra-wacko that Trump is still trying to pin the Flynn mess on Obama, but if Trump just discounts everything Obama and anyone associated with him says (not an "evidence" kind of guy), then whatever they say, and whatever evidence they provide, won't mean anything.
4) Trump hates backing down. Once Flynn was in Trump's orbit, to kick him out in response to Yates and Obama and the others telling him that the guy was compromised would be an admission of error, and Trump can't do that. EVER. That's why, even now, he's blaming Obama for him (Trump) having hired a guy as National Security Advisor that Obama told him not to hire.
Yes, we can still tell a story about how this fits in with the Trump-is-Putin's-bitch hypothesis, and the Syria bombings don't completely debunk that since things have calmed down on that front (something I posed as a possibility if Trump is in Putin's back pocket in April). However, there are a lot of other possibilities here. We still don't know what the deal is with Putin and Trump. Flynn? Yeah, that guy is probably crooked in addition to being absolutely batshit fucking crazy, and Trump was an idiot to hire him as well as way too slow to fire him, but we still don't have a clear picture of what is going on here. That's the problem with trying to analyze a stupid person. There are always too many possibilities for how stupidity works.