Not every one cares so much about a sticker. It's not like the quality of parts is different.
If I was looking at two identical bikes, and one was Name Brand, and one was Bikes Direct.
And I then noticed the BD was considerably cheaper. I would go for the BD.

Then again, a lot of LBS's give service plans out with there bikes as long as you own it, if the increased price for a name brand is worth that for you, than by all means.