It is not wise.
I think that if your charity gets $1M/month (or even $100K/month) in donations, it would be prudent to have a (good) accountant oversee your operations, and use a proper FDIC-insured banking system.
I'm aware of a company who was using PayPal for retail sales and got stuck with hundreds of thousands of dollars on their PayPal account and could only withdraw hundreds (500, in fact) every day. It took some time for them to recover the money, and with some pressure too. Admittedly, the company used PayPal incorrectly, but have you read their terms and conditions? Not sure if using them "correctly" is even possible.
You can use e-check, merchant accounts (Square for example will ACH-deposit to your bank) for credit cards, etc.