My understanding (from a friend who was in the bicycle industry for many years) is that bikes typically have about a 30-35% markup from dealer cost to list price. A $3000 retail bicycle costs your LBS about $2000-$2100 plus floor plan costs (the interest to finance inventory), handling/assembly/prep costs, etc. That means if they sell you that $3K bike for full price their gross profit is probably in the $800 range. Pretty healthy at that point. But many bike shops do discount. I got my $4600 MSRP bike for $600 below retail cost. And that means the dealer still made $600+ on the unit. But that $600 discount was about half the profit built into the bike's price.
Bike shops make MUCH more money on accessories like bike jerseys - which typically have 100%+ markups (i.e. an item that retails for $100 cost the shop $50 or less).