There are shuttle buses (Central area C, where you also find the railway counter to get the ticket to Regensburg) to Freising station where you can catch a train to Regensburg (about 100 minutes, ca. 20 Euro for bus and train). These trains depart at Munich station about 15 minutes earlier.

There is a direct bus transfer service “airportliner” from Munich airport to Regensburg and back (further information at http://www.airportliner.com), travelling time about 100 minutes. Price: 29,- Euro one way.