E Rail in Germany

Rail Europe is an American travel agency (although owned by French Rail. They don't run any trains in Europe. Neither does Eurail run trains. Eurail are a consortium of European National Rail companies organized to package and market rail passes. About the only ones in Europe that run trains are national rail companies and their subsidiaries.

German Rail trains (S-Bahn) do go right into Munich airport, and German Rail (S-Bahn, regional and express) trains go into Frankfurt (through, actually). In Munich, there are two S-Bahn tracks used by commuter trains into town, one around to the east and one around to the west. They both take about the same about of time; you just take the next one leaving.

At FRA, there are two stations. The Regional bahnhof is close, underground, under the building across the access road from Terminal 1. It handles S-Bahn and regional trains (and the occasional IC). Farther out, on the other side of that building, across the Autobahn, the Fernbahnhof handles the high speed express trains.

You can also search using the three letter airport codes (MUC for Munich and FRA for Frankfurt) to find trains to/from the airport train stations.