I had a big problem with bubble algae... and to be honest, I came home from work/school one night and lost it. I ripped/popped almost every single one I could find, knowing the spores would spread, then vacuumed it all out... I really didn't care anymore.
I had bubble algae because I hadn't changed the water in forever and even used tap water at one point. I recently bought an RO/DI system and added a fuge with Chaeto. The bubble alge hasn't returned since.