L.D.
I think the theory is that the wheat that we have available now has been highly engineered to make it more glutenous and, therefore, more appealing for baking, etc. It is not the same wheat flour that our parents (at least mine) and grandparents grew up with. Unfortunately, our digestive systems have not evolved enough to handle this new type of wheat. There are a number of conditions, not necessarily childhood conditions, that are believed to be -- or known to be -- associated with wheat/gluten consumption like celiac disease, crohn's disease, hashimoto's disease. And then there are a number of parents whose children who have ADD, ADHD, autism, asthma and allergies who swear that their children's health improved after they removed the gluten (and other things like artificial colors, etc) from their children's diet.
Now, there's a distinction between food allergies and food intollerances. Some food allergies do take time to build up but they usually end up being an immediate reaction type of thing like what you see with a nut or shellfish allergy. With food intollerance issues, this is a little bit more commonplace and they are a little bit more subtle in how the sypmtoms end up manifesting. Tell-tell signs that a food intollerance are an issue include the following: Red checks not long after eating the offending ingredient; Diarrhea or constipation issues; Excessive gas; Kind of out of behaviour; Bits and piece of the offending food in the person's poop that was not able to be digested. Food intollerance issues come and go throughout a person's lifetime and it just basically means that your body has a hardtime breaking down the food and using it as energy. For some, excessive exposure to these kind of foods can be very destructive to their digestive track and can be leaked into their system and end up being perceived by their body as an antigen that needs to be attacked and destroyed.
I know this all sound very convoluted and, frankly, it wasn't more than a year ago that I thought this was all a lot of rubbish but my son has been gluten free for almost a year now and it has really helped him with a number of developmental delays that we were experiencing with him. There have been a couple of times that we have allowed him to have something with wheat in it during the last 11 months and had lived to regret it. If you wish to learn more about this issue, there's a very good book called Gut Solutions that is available at Whole Foods and probably at Barnes & Noble and Borders as well.
I hope this answered all of your questions. Good luck.