I think Flynn was just the first act of the intelligence community in retaliation for Trump attacking them. I think it may be repeated many times. Just goes to show you: Don't screw with the spooks. They are 1000 times better at it than a dope like Trump and they probably have dirt on every one in his administration.
Now several of his nominees have failed or dropped out of the confirmation process even with a sympathetic Republican majority in the Senate. Think Trump just picked really bad nominees? Or did the spooks leaked information to selected Senators?