In my case, this wasn't a problem. I chose to get into the market specifically to sell FBA. As such, I knew cheap items were not viable for FBA, so I didn't sell cheap items on it.
That minimum commission fee is the reason you don't see anything on Amazon for below $6 (unless there's some weird accounting going on for the seller). Above $6, the fee turns into a percentage and is easier to manage.
That fee is also the reason you'll often see packs of 3 or some item when you only want 1... it's just not profitable to sell the 1 at a reasonable price anymore.
As an aside, the SNL program doesn't get all the same benefits as FBA. In some cases you don't get the Prime badge, and in other cases you're an "Add-on Item" to get free shipping for the buyer.