The angry orange boy running the country has a 50+ year history of being a bully that can't take any critique whatsoever. Not sure he has anything to do with the FCC decision, but it would be in character. 
Colbert has responsibility to his audience, his boss, and yes, the FCC. So ..... he made a poor joke, .... kinda crude for TV. (you ever see these guys in their live shows? Even the female comics are brutally crude) No one was harmed in the making of this joke, no one died. It was on TV late enough that kids shouldn't have seen it. 
On the other hand, the orange boy has a nation that he is responsible for and if you believe the hubris, his position as leader of the free world. Every day he says things that are for more offensive and dangerous than Colbert ever thought of being.... 
Whats scary is the administration's seeming need to control the media and discredit/destroy any portion of it they can't control.  That's what everyone should be worried about, not Colbert.