I don’t think it’s anything to worry about. I was learning a tune that used the thumb to play in the F-sharp position of the E string, just that one note followed by an arpeggio on some of the open strings. In that instance it was convenient and easy to use the thumb. Other than that, I think I would find it difficult to play with the thumb while forming a full or partial chord, so I usually look to play conventionally. I don’t think there are any hard and fast rules, just go with what’s more convenient.
I don’t think I’ve seen any lessons on here that use the thumb so don’t worry about it. Don’t forget that Hendrix played with his teeth! I bet there’s not many lessons in the style of Hendrix that will encourage you to do that!

Have a look at this blokes fingers, built to play guitar or what? If we could all have his attributes there would be no problem in what we are trying to achieve.
http://www.youtube.com/watch?v=BhU15PmQtZM