Off the top of my head, SpongeBob SquarePants, Danny Phantom, Fairly Oddparents, The Big Bang Theory and It's Always Sunny in Philadelphia all have jokes, if not the main plot point of the episode, that are just mocking the existence of LGBTQ people.
Definitely agree. How they handled the pilot episode was much better, it was all about CIS-male fragility. I think the creators regret how they treated that character though.