Although short connections (eg: 6 mins) on DB generally work (I guess otherwise DB wouldn't sell them?), they can easily be missed - especially if: there are lots of you, with luggage / you're not familiar with the system / it's winter (and so trains are more likely to be delayed).
Note that you can set the journey planner on bahn.de to allow more time for connections (under 'Further search options').
I assume the 6 minute connection you're looking at is the one via Plattling. If you set a minimum connection time of 10 minutes, bahn.de gives you a similar, but slightly longer, journey with a 13 minute change in Regensburg (instead of Plattling). This is a bit more reasonable - but could still be tight (as in Regensburg you'll probably have to go up and over a bridge, and it often seems to be quite crowded - I don't know what Plattling is like in comparison).
As stut has said, even if you're on an inflexible ticket (as long as it's the same ticket for both trains) then if the first train is delayed and you miss the second train, you'll be allowed to take the next available service.
However, I would still advise against the connections via Plattling or Regensburg. These take you on the ICE line that runs from Nuremburg to Vienna. However, there is only one ICE service every 2 hours on this route - so if you miss the connection, you'll be left waiting 2 hours for the next train.
Much better to take the direct Railjet from Munich to Vienna (which I think is also every 2 hours).
For example: the ICE connection via Plattling leaves Munich Hbf at 08:24 and arrives in Vienna at 13:22. Meanwhile, the direct Railjet leaves Munich 1 hour later, at 09:27, but arrives in Vienna only 20 minutes later than the ICE, at 13:44. (Or the same minutes past the hour, every 2 hours later).