I don't want to put words in their mouth, but a big part of the reason is the very protection you talk about. If it's put on a credit card, you can always dispute the charge with the credit card company, possibly delaying the payment, or even avoiding it. With the bank account, the money is withdrawn immediately and is a lot harder to reverse.

Now if it were the individual vendors, I could understand that better, as they are often small businesses with tight cash flows. But this is Paypal itself doing this.

I feel the same frustration of always having to answer, "Yes, I'm sure I want to put it on a credit card."