Austin has a great reputation, but it's still in Texas.
There are homophobic troglodytes everywhere. However, it is verboten to be openly rude about that sort of thing in all but the most repressive and tiny communities. Those are the ones that creep out straight white males like myself, let alone minorities of any kind, so barring a flat tire I don't think you'll end up there by choice anyway. Actually, being atheist is something I tend to keep to myself, too.
And actually, a lot of rural areas (which is, geographically, most of the state) have hippies in disguise all over the place. The small town of Kerrville is home to a huge hippie music festival every year; Fredericksburg is near the infamous Luckenbach, where Willie Nelson still shows up occasionally; and places like Wimberley are hidden in the sticks but have wiccans and sell quasi-spiritual swag and incense in the local shops.
You can definitely sense a cultural contrast outside of Austin.
Seeing people smoke pot openly in the streets still messes with me.
That's a long way of saying that, based on my second-hand experience, gay men don't run into trouble in and around Austin or its immediate suburbs.
I've had many gay coworkers and they usually stayed close to the city (I live in the DFW area).