Well, foxy is so easy to implement into any existing site it would be a good option for most small sellers looking to sell on the web...unless you’re a programmer and looking to develop your own system to emulate a foxycart-esque environment.

Foxycart allows you to choose a payment method whether it be Authorize.net, PaypalPro, or Paypoint, etc. I thought the FoxyCart monthly fee prevented the individual seller from having to deal with individual transaction fees, but this is apparently not the case.
Paypalpro will charge you a monthly fee of $30, then about 2.9% + .30 per transaction.
Foxycart says this on one of their pages:
For what it’s worth, we at FoxyCart generally recommend CDG Commerce for most merchants in the US. PayPal’s Website Payments Pro is also a decent option, though the monthly fees are higher.
CDG is a monthly fee of $10 and 2.25% per transaction, which is much lower in the long term.
I think you’re going to run into fees at any site, but I think Paypal is somewhat high, though I have no real e-merchant experience with payments and transactions etc. I would suggest looking into the different methods Foxy offers and their fees associated.