Yes they are because the big networks only want to do business with big business. Shareasale is the least expensive of the big networks, but it still sticks you pretty hard.
I would imagine that with the current economy and the huge number of networks, you should be able to shop around and cut some pretty good deals as long as you don't want to go with one of the major networks.
As an established merchant with a good reputation you can sometimes negotiate the commission you pay the network, usually by offering AMAZING payouts to their publishers. Generally though you pay a % of your payout to the network. If you are using a performance network you only pay for results, and a good network won't charge you additional fees to sign up, etc.
I find it amazing that some networks charge the affiliate to be in the network. I would definitly suggest looking for a network that is free for the affiliate to join. One of the ones mentioned above or eComLeads are good places to look.
No respectable CPA network will charge you to apply or be accepted as an affiliate. We make our money only when you make money by getting leads to our offers.