Part of the drivers for eBay was that Skype was at the time (apparently) responsible for something like 90% of paypal signups (especially outside of established markets like the US).
I think they were worried that if Skype had been purchased by Google, and they switched to using Google Checkout rather than paypal, that they would have lost a lot of market share.
Wow, 90% seems like a lot... although I can't seem to find a source for that. According to an answer on Amazon's askville [1], the total ended up being ~1.7% around Oct 2006.
At one time, the life cycles of the companies might have aligned (as Skype was taking off, and Paypal was plateauing) to show ridiculous numbers like that. Still, it seems hardly justifiable to pay billions to buy a company just because they use your service for checking out.
I think they were worried that if Skype had been purchased by Google, and they switched to using Google Checkout rather than paypal, that they would have lost a lot of market share.