Those fees are on top of the cut that Authorize.net/PayPal/Protx take, right?
So with Paypal Website Payments Pro for example the total cost would be $49/mo and 4-6% + $.30 per transaction.
Yup, that is correct. One nice thing, though, is that you have gateway portability, so you can do some hard negotiation with your gateway and/or merchant account once your volume grows to cut down on the fees. And, of course, as your volume grows, you'll be getting charged 1-2% for most transaction. 3% is only for the first 50 every month.