( As others have already said, PPPoE is literally PPP over Ethernet. And similarly PPPoA is PPP over ATM. )
Ethernet and ATM are oddities in the networking world as they define both a layer-1 and layer-2 component. In the case of ethernet, it's layer-1 has always used it's layer-2; no one ever built it any other way. (Ethernet's layer-2 protocol, however, has been used over many different layer-1's. For example, 802.11 WiFi, DOCSIS.) ATM went the other direction; it's layer-1 is virtually unheard of, but it's layer-2 can be found lots of places... T1, T3, SONET (OC-X), sync-serial (V.35, HSSI), ADSL, etc.
PPP was invented in the era of async-serial (RS-232) and dialup modems, and runs "naked" on those physical layers. As technology advanced, network operators wanted to continue using the same "dialup era" infrastructure and processes (i.e. account management), thus methods of carrying the familiar PPP were needed. An ethertype was registered for transporting PPP frames over ethernet. (and similar processes for ATM, and SONET. In the case of SONET, a bit of HDLC was needed to make the framing work with the SONET NRZ encoding.)