A few reasons.
Firstly that is just the way it has always been and ISPs are loath to change a working setup.
Secondly it's possible to create translators between different types of PPP. Just because what your router sees is PPPoE doesn't mean the path all the way back to your ISP is a simple ethernet network. You might have a setup that is PPPoE from your router to your modem, PPPoA from the modem to the DSLAM and L2TP back to your ISP.
Thirdly PPP provides identification and authentication. This is important for a few reasons, firstly to allow robust identification of abusive users. Secondly to allow multiple ISPs to operate over the same broadband access network. Thirdly to ensure users who have purchased packages with static IPs get the correct IP.