That is not how the tax works. It taxes gross receipts, in this case meaning Paypal's fees, not its total payment volume processed, because it only applies to amounts that would be considered income to Paypal for federal income tax purposes. Furthermore, the tax is allocated based on payroll, meaning that the tax is prorated based on the % of employees based in the city of SF vs elsewhere.

Paypal reported net income (i.e., profits) of almost $4 billion last year on roughly $25 billion of revenue on roughly $1.250 trillion of payment volume. Only approximately 550 of their 26,500 employees were located in the SF office, meaning that their effective GRT rate would have been .016%, for a tax of roughly $4m, or approximately their costs for 10 employees. They can afford the gross receipts tax.