I have three sites that accept money.
The large one, has its own merchant account: the cash flow is monthly recurring billing. We also accept Paypal but only under certain conditions.
Site number two only accepts PayPal. That seems to work fine. It's single payments for $100.
Site three has a Paypal merchant account. It also works fine and the costs seem lower than on my other merchant account. It is primarily $25 and $50 payments.
I'm trending towards doing it all on Paypal. The big problem with them is the reporting is so poor so far. I assume that they'll get better at it.