Except the FCC literally threatened ABC over this

Read the comic again, your right to free speech has nothing to do with your privilege of using the public airwaves. The FCC chairs' threat to ABC is about the later, not about arresting executives or Kimmel like one would expect if you read the comic then your comment.

What was wrong with what Kimmel said?

Is it against the public good to question the motives of the president of the United States?

Is it misuse of public airwaves to point out the lack of evidence on hand to divine the political affiliations of this school shooter?

The comic is incomplete, the first amendment also protects content based discrimination in government interactions outside of certain exceptions. It does not require arrest.

For example in the granting of permits for marches.