Is it possible to take a train from Salzburg and get to Munich airport for an 11am flight?
Yes. I would suggest you take the 05:45 am train.....has 1 change in Munich OST ( 23 mins ) and then to Airport arriving @ 8:15 am. This will allow for 2 hours to check in, etc. Austrian Rail Site: http://www.oebb.at/en/index.jsp The site will tell you the type of train and the arrival platform in Munich OST and your departure platform in Munich OST to Airport. When checking schedule/timetable....enter time as 05:00 and click on a date 4-5 days ahead until you know how to work the site. Also click on "Show Intermediate Stops".
I think I would use the German Rail (Bahn) website to schedule this trip, which is almost entirely in Germany. Try to use the same type of day, ie weekday, Sat or Sunday, since schedules sometimes vary. That 5:45 train is a more expensive IC. I would probably take the 6:09 RE, which connects with an S-Bahn in Ostbahnhof and gets you into the airport at 8:55. That way you can use a Bayern-Ticket (22€ for one, 26€ for two) all the way to the airport. However, I know where I'm going and have only a carry-on, so I could do it in two hours; you might want to spend the money and have more time. The other thing you might want to consider is going to Munich the evening before and staying in Freising. From Freising Bahnhof it is a 20 min, 2,50€, bus trip to the airport. You can find accommodations at www.freising.de. You can get to Freising with a Bayern-Ticket. Take an RE from Salzburg to the Munich Hauptbahnhof and the S-1 from there to Freising. Pay attention to the end of the S-Bahn you board. The train splits in Neufahrn. The back half goes to the airport; the front goes to Freising.
Agree with Lee :).