Oh, completely and it's hard to compare it to the superhero world. Yaoi fandom has kinda taken over, but the earlier classic examples of gay characters in primarily shoujo and josei comics (mainly for and by women), though are much more about characterization. Unfortunately a lot of that hasn't been translated--classic manga doesn't sell well here, but some titles have. Two of my fave examples:
Banana Fish by Akimi Yoshida is a brilliant crime drama that ran in the late 80s about a New York street kid (the depiction of 1980s New York is pretty hysterical) and a Japanese teen who gets sucked into his world. It's out of print in English but one of my fave comic titles ever.
http://en.wikipedia.org/wiki/Banana_Fish Moto Hagio is regarded up there with Osamu Tezuka as one of the masters of the genre, and the first woman who back in the 70s really gained a male readership, and her work deals a lot with gender and sexuality (particularly her sci fi work which is influenced by Ursula LeGuinn, as well as her masterpiece A Cruel God Reigns about a college student who was sexually abused as a teen by his step father, and then meets and develops feelings for his step brother at Oxford). Her works are just starting to be translated--Fantagraphics has a deluxe edition of her first hit, The Heart of Thomas (influenced by the French film Les amitis particulires as well as Cocteau's work).
http://www.fantagraphics.com/browse-shop/the-heart-of-thomas-aug.-2012.html?vmcchk=1 She's my favorite comic book artist/writer ever (luckily much of her work was translated in French).
But even in modern boys comics, sympathetic gay side characters are pretty present, and of course seem to exist in nearly every shoujo manga. Yaoi gets all the hype, especially here, but is a pretty small representation of gay characters in manga as a whole, even if it's started to dominate translated titles here.
*sorry--that was kinda a rant*