I don't know, I don't think something isn't homophobic simply because it wasn't meant as an insult against homosexuals. When someone calls a man a "pussy", they probably aren't even thinking about women or where the insult originated, but it hinges upon the premise that being a pussy - which in this case obviously implies female - is a sign of weakness and inferiority.
Calling something 'gay' as a general insult doesn't really involve gay people per se, but it's rooted in the belief that being gay is wrong. Calling someone a faggot because they're pissing you off, and not because you're accusing them of being gay, still comes from the idea that being gay is something reprehensible and can be used as a general insult.
I think it perpetuates the discriminative culture, even if it isn't trying to actively insult a minority. A lot of the time when people are repeating these jokes and insults, they're not trying to hurt the minority upon whose perceived wrongness the joke is based, but they're still validating a certain worldview, a certain discriminative belief, and I don't think that's okay.
I think the term 'homophobia' is deceptive in how it implies some sort of fear, namely the fear of being gay, but while for many people there is such a fear, for many others it's really just hatred. It's not about being scared of being gay, it's about disgust for someone who's not like you, who's outside the perceived norm, who's not like what your pastor says people should be like, who challenges the status quo, who's just not like what you're used to. My aunt once told me that she thinks gay people are gross, because when she sees a man and a woman together, she thinks that's nice, but 2 men together seems unnatural and disgusting, and so shouldn't be happening. There's no fear there, there's just conditioning and seeing the world in stereotypes. Maybe 'bigotry' would be a more apt term, since 'homophobia' has such questionable etymology. But since we generally use 'homophobia' to describe bigotry toward gay people specifically, that's kind of what we're stuck with here.
As to Colbert's comment, I do think it's both homophobic and misogynistic, even though he likely did not mean it as such. Obviously we know what he meant - he meant Trump was submissive to Putin, he did not mean Trump was gay. But it's rooted in the idea that anyone sucking cock is submissive, servile, with no free will. I don't think it's about the sex act itself. It's about the fact that sucking cock is something perceived to be done only by women and queer men. And those are the people our society views as inherently lesser. The reason these kinds of jokes exist is that our society believes that a straight man is the only truly respectable variation of human, and anyone else is inferior. A straight man would never suck a cock, you see. Only a queer man or a woman would be doing that, so comparing someone to them automatically implies their inferiority.
So, ;tldr, Colbert probably didn't mean it as homophobic, but I do think it is homophobic in nature and perpetuates homophobic mindsets. His apology was pathetic. He apologized for the words he used rather than the implications he made, and while I don't exactly expect comedians to be politically correct, I don't think someone should call themselves an ally, but then continue to make jokes rooted in bigotry.
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Also, am I the only one who finds these kinds of comments a bit rapey?Like, if you assume someone won't enjoy sucking dick but you tell them to do it anyways, you're basically suggesting that you dislike them enough that you hope unpleasant sex acts occur to them, most likely against their will...
I totally agree.
I'm reading through the first few chapters and I'm liking what I am reading so far.* Love the artstyle and the story is cute so far. Thank you so much! 
