It may be an individual thing, but I did just as well with generic Protonix. I noticed no difference at all. My doctor was a bit reluctant, and stuck with the brand name version, but one time they were accidentally filled as generic, and I didn't notice a thing (except that I had more money afterward!)
It wouldn't hurt to try. Is your doctor worrying about the switch to generic?
I do have a friend (without GERD) who has difficulty with generics. I guess they can have different things binding them together, which may make them more difficult to absorb. (That's what my doc said.) As I said, I never noticed a bit of difference.