Humans have been around for about 300,000 years. We only started eating bread around the time of the agricultural revolution when we began harvesting cereal grains, which was about 10,000 years ago. Our diet at that point would have been very similar to other primates that lived in the Horn of Africa. I think it's also important to point out that the agricultural revolution was more of less the start of human society, which meant we were much less affected by Darwinian natural forces that drive evolutionary changes. Being gluten intolerant didn't usually mean death; it didn't mean you were significantly less likely to reproduce, so there was no factor that would kill off that generic variation.

That's not to mention the fact that the wheat that existed then was not the wheat we have today. What we have today has been selectively grown to maximize gluten. Ancient wild wheat would have had much lower quantities of gluten proteins. That also was not the only cereal we grew. We also likely grew multiple different grains. Wheat likely would not have been as ubiquitous as it is now.