paypal was originally for
ebay, i think it's owned by them. it then became a convenient way of payment for online retailers, usually smaller ones... could be paypal has a lower charge system.
Amazon are always trying to get me to have one of their credit cards. also, ebay could be seen as a rival to amazon, so it's doubtful they'd use paypal for that reason.
there are also other aspects, such as insurance for failed transactions/theft that favour credit cards for the bigger companies. those would outweigh the additional service charges.