When I'm buying something, whether it's aquarium livestock or supplies, a pair of jeans, or whatever, if I know that I can get the same thing somewhere else for less than half of what a place is charging, I'm going to get it at the cheaper place.
If I'm looking, for example, for an new light for my aquarium... someone earlier on this post stated that they saw some lighting equipment in a store for $1500- if I know I can get the same thing on-line for $500, I really cannot justify paying 300% more at a LFS. But on the other hand, if I see a tank-raised specimen at a LFS for, say, $25, & I know I can get the same thing, also tank-raised, on-line, for $15, I'll probably just buy it at the LFS, because I won't have to pay for shipping, I can see the specimen before I buy it, and I can talk to a store employee, ask questions, etc.
What it boils down to is what people are willing to pay for the personal service you get in a LFS. For me, paying an extra $10 is worth it, but paying an extra $1000 for some lights is definitely not. I realize that it is very expensive to run an LFS, and that the overhead is a LOT more than that of an on-line store, but I, like most people, don't have that kind of money to just throw around. What some people consider a reasonable mark-up is relative- it depends on how much money they make, how expendable their income is, and how much they are willing to pay for certain services.