If your ability to handle credit cards is costing you more than your margin, then you're in the wrong business. If your margins are that small then you need to rethink your business plan.
As to PayPal, the thing most people don't understand is that PayPal is totally up-front about all their fees, and they charge one rate for everything. But, as you mentioned above, a more traditional payment gateway charges all kinds of different rates for different cards, and in the end often culiminates in costing more than PayPal's flat rate structure.
If the majority of your transactions are very low-priced purchases, you might explore PayPal's micropayments option, which is supported in Zen Cart v1.3.9 by making a few tiny configuration adjustments. Not sure how it handles subsription items.



