We recently flew to Prague with a 1.5 hour connection time in Munich, and the screening line was so long (and only 2 screeners) that we were anxious about missing our connection. (As it turned out we had 10 minutes on the other side before boarding began.) Our friends routed through Frankfurt with a 1.5 hour connection time had to be pulled out of line to make it through screening timely.
Bottom line - if you have a connection, I would advise making it 3 hours or more, to avoid stress. Even if both legs of the journey are on the same ticket, and the airline is "responsible" for getting you to your destination, their solution of a next flight may not suit your travel goals.