Countercultures have always been "cool" - the rejection of the dominant culture is part of their cool factor. Some of the most memorable aspects of recent Western cultural history are counter-cultural: hippies, punks, slackers.

A counterculture isn't defined by whether or not it's considered cool, but by whether or not it is actively participated in and shared among the majority of people. Queer identities may have a lot of public support (and even that's debatable), but queerness is not part of most people's lives. Western societies are still cis- and heteronormative. Queer culture is an other, not the mainstream.