Good location for transit in Munich

Look for lodging around the Munich Haupftbanoff. There is local, national, and international transport around there

We stayed at the Mercure Altstadt, about a half mile away (because we had points to use). Anywhere in the Altstadt will work. If you don't want to walk all the way from the Hauptbahnhof, look for a place close to one of the sbahn stops at Stacchus, Marienplatz, or Isartor. You can use a site like booking.com. and filter for your preferred area, budget, amenities, etc.

I don't like the area closest the the HBH; it's not dangerous, just sketchy.

I'd say stay around the Viktulienmarkt. Easy S-Bahn to Hauptbahnhof from Marienplatz, and you can get off there on the S-Bahn from the airport.

My first suggestion would be Freising. It's only 20 minutes by bus from the Munich airport, and there is a direct RE from Freising Bhf to Passau in under 2 hours. Freising is the home of the Weihenstephan state brewery; in warm weather you can enjoy a meal in the shade of their outdoor beer garden.

Here is an English list of accommodations in Freising.

"...but also be near the train station...." That's where I stay in a Pension close to the Hbf.....very convenient, I don't have to rely on public transport let alone a taxi to get me back to the Hbf on departure day. There are numerous small hotels and Pensionen near the Hbf on Schillerstraße and Goethestraße.. There is also a 3 star hotel across from Hbf on Bayerstraße....Europäischer Hof.

There are numerous small hotels and Pensionen near the Hbf on Schillerstraße and Goethestraße.

This is the area previously described as "sketchy". Just one or two strip joints and a few slot machine establishments. Nothing to worry about.

If you stay elsewhere, not walking distance of the Hauptbahnhof, and you travel after 9 am M-F, anytime Sat or Sun, a Bayern ticket will allow the use of the local transport system to the Hbf and passage on the hourly Regional Express train to Passau for 31 EUR total for 2 people.

There are several hotels around the Munich East (München Ostbahnhof) stations, including one of the Motel One chain (my personal preference). The S8 to the airport stops at the Ostbahnhof, and the neighbourhood is much nicer than around the Hbf. It's a 5 min. S-Bahn ride from there to the Marienplatz.

The frequent s-bahn stations in the corridor between Ost and Pasing mean that nowhere in that area is really far from the station.

King's Hotel. 5 minutes from Hauptbahnhof.

I agree with sla and Nigel that there is no reason to stay near the main train station as public transport near the Altstadt or on the SBahn line between Ostbahnhof and Donnersbergerbrücke is very good. Normally I recommend the motel one Ost, but with only one night and desire to “experience some of Munich” your best bet is to stay in the Altstadt area. I would recommend Motel One Sendlinger Tor here. It’s just one subway ride from the main train station.

DJ

Yes, otherwise as Lee suggested, and stay in Freising and take the S-Bahn into the city for afternoon and evening, then back to your hotel in Freising where you can pick up the direct RE to Passau in the morning.

If you want to stay in town, I would suggest Pension Lindner. It's only a couple of blocks from Marienplatz, which is the heart of the city. From the Marienplatz S-Bahn station, you can get to the Hauptbahnhof tief (deep) S-Bahn station and come up the escalator and catch the regional train to Passau in just over 2 hours. If you leave after 9 am on a workday, you can make the entire trip, Marienplatz to the Hauptbahnhof to Passau with a 31 euro (for two people) Bayern-Ticket.