Before I get into this, I should "warn" you: I'm a game (and comic book, and SF&F book) store co-owner.
As has already been pointed out, Amazon and the other major chains get a larger discount than your FLGS. Publishers (and distributors as well) base their discounts on how much you order from them - the more money you spend, the cheaper the individual items become.
Another reason Amazon and Barnes & Chernobyl and such can offer the discounts they do is the HUGE volume they sell. The fact that their profits are spread out over a huge selection of stuff - if they lose money on one thing, they'll make it up on something else - helps as well. And, by the very nature of being a chain, if one store doesn't make scads of money, they have a bunch more to pick up the slack
Plus, those guys have almost literal tons of cash to tide them over through short term loses.
Keep those things in mind: The FLGS doesn't get the same discount as the big guys, they don't sell as much "product" as the big guys, and they don't have the safety nets the big guys have.
Now, I never used to believe that discounting was a bad idea. Then I did a little math...
If a store orders 10 copies of a $30.00 book and they get a 50% discount (which is on the generous side, but it makes the mat easier), that means they've spent $150.00 with the potential of making $150.00 if they sell all of them.
Now let's say the store offers a 30% discount, that means the store would make $60.00 if they sold all the copies they ordered. Still a profit, but drastically less (which, in and of itself, WILL make a difference).
That profit on the discounted books hinges on selling all of them, though. If things go very badly for the store and they only sell half of the copies they order (for whatever reason), the profit disappears.
10 copies of a $30.00 book purchased at a 50% discount cost the store $150.00.
The store sells 5 copies to customers at a 30% discount, and the other 5 copies sit on the shelf.
The store has "made" $105.00.
In other words, the store has actually LOST $45.00.
To make any money in that scenario, the store HAS to sell at least 8 copies - and then they make a massive $18.00.
Okay, I'll go away now.