Funnyjunk is most likely being reported as malicious because of the sketchy online advertising program it's been using. Specifically, they probably ended up accepting an advertisement that contained malware .
My reasons for believing this are so:
-I have common sense, that's the logical answer.
-All advertisements on FunnyJunk are currently being blocked by Firefox and most likely other any other browser that's blocking FJ in the first place, without the need for an AdBlocking program.