I think that the mark up is around 30%. The mark up on shoes is 300%. I buy stuff from 2 LBSs all the time. Don't begrudge them the money. Most bike shops need that / count on bike sales to pay for all fixed costs. If you buy stuff all the time and get to know the owner, they might cut you some slack. Especially if you know just what you want and you dont seem like the type to come back later and be a pain.
The real money maker in the bike business is the importer. Its only one guy for like 90-95% of the whole damn US market. He basically specs the bikes in china, gets them to put it together in accordence with what folks will buy and us saftey regs.
If you really want to save, buy used.