I'm not entirely sure of the cost to set up merchant accounts so someone can correct me if I'm wrong, but I believe to actual accept credit cards without paypal or another organization it requires a hefty fee along with monthly payments. If I am wrong, then please correct me, I'm interested in how this works
As for using paypal, it is realy easy to set up a merchant paypal account and start recieving money from customers; however, the only catch is that if you recieve too much money, then they take a fee from you per dollar. I think it is somewhere aruond 1,000 dollars before they start taking a percentage of your money.
If you read the tuts at paypal then setting up online payment with paypal can be a breaze, especialy if you take insaniac's advice and use a module such as Business::PayPal. Just look into it and figure out how you want to do it. Paypal is probly your best bet if you don't know how to set up ssl and other encryption methods or you are fairly new to Perl