Yes, the PayPal fees DO add up but what is the alternative really? There's nothing quite as fast, trusted/accepted, and easy to use...
Those fees are tax deductible though as a banking expense (I think that's what it's classified under) - and you can download comprehensive monthly, yearly, and tax reports from your account to help make bookkeeping easier (under the HISTORY tab when you're logged in).
AND, if you're taking in more than $3k each month you can actually LOWER the percentage that you pay on each transaction.
Here's how.