One problem I've encourntered with such endevours is buying a guitar with the intent of flipping it, then falling in love with it and have a hard time parting with it...
Well... that's what usually happens to me.
Flipping is fine once in a while with a really great deal - but those are hard to find. Using your cash to try out great hear on sale and then selling it and coming out slightly ahead is a wonderful feeling. Its not that you make that much money, but you get to try out stuff etc.
I don't have time now to mess with ebay, potential problems, setting a guitar up, etc. etc. to make $50 in the end after all fees. If you have the time, and enjoy above said activities, go for it. You will soon learn if you were born to be a business-man or not.