I've bought 5 guitars online (2 of them off Ebay)-- never had a problem.
I know there are lots of people who say you have to play many guitars and find the one that "speaks to you." I think that's BS for the most part. Every guitar I have bought online has "spoken" to me once I started playing it. If you get the exact make/model/color of guitar you want, then you will fall in love with the guitar regardless of whether you actually played it before you bought it. On the other hand, if you are unsure about what kind of guitar you want, playing many different guitars is a good idea.
Granted, every guitar is different. Wood is variable. Two Fender Strats made with the same kind of wood by the same human will sound slightly different. But they both will still sound and feel like a Strat. However, I don't deny that there are "special" guitars out there somewhere.
So, if you want to spend countless hours searching music shops, pawn shops, garage sales, classified ads, etc. looking for that "special" guitar-- I say go for it! Meanwhile, I'll be at home becoming a better guitarist by practicing on the American Strat I ordered online.
I like ordering online. I get the exact guitar I want (color, etc.) and I get a guitar that no one else has played before. You usually cannot say that about a guitar bought from a music store. How many hacks pounded on that "special" guitar before you bought it? Also, with the very liberal and easy return policies most of the online stores offer, it's really a low-risk transaction.