I don't think there's any solid reason to avoid whole-grain wheat products. Wheat, however, has acquired a bad rap largely because of other "alternative" health ideas, notably food allergies, "yeast", and naturopathy, and more recently "paleo diet" and blood type diet notions. Many, if not most, practitioners and writers in these fields demonise wheat (along with other common foods such as corn, soy, many types of fruit, fermented foods....) claiming various ill effects ranging from population-wide "allergies" to fermentation in the body, and also saying that the highly-refined presence of such ingredients in virtually all processed foods has made us (the larger "us") more reactive to them.
Mostly crap, I think. As atherjen says, it's a grain, so in a less-processed state it has the nutrients of other grains. If you are doing a competition diet, or something of similar precision, you may want to watch your personal reactions to it and see if it bloats you more than other carbohydrates -- but even then, that's not necessarily a reason to shun it during more relaxed periods of your life.