The reason that people suggest you not eat bell peppers raw is because they are a nightshade plant. Nightshade plants have a chemical designed to poison insects which might try to consume them...when you eat a nightshade plant you consume this chemical.
Of course we are much bigger than an insect so it is not so harmful for us, but many individuals do have problems with nightshade plants, especially those with arthritis or other immune system illnesses.
This article on nightshade plants will give you the full scoop on them...hope it helps.
http://www.squidoo.com/what-are-nightshade-plants-tomatoes-potatos
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