If you are coming in late and just want a place to sleep before catching the train the next day, I think Ken's suggestion, Hotel Royal, is an excellent one. If you have a little bit of time and want to see some of Munich, then I would suggest you stay at Pension Lindner. Lindner is located just a few blocks from Marienplatz. If you think Marienplatz is too far a walk from the Hbf, there is an S-Bahn almost every minute from the Marienplatz station to the Hbf (3 minutes, 2,80€/person or less).
If you haven't already purchased your ticket to Venice, specify from Marienplatz with a change at the Hbf. The price is the same and includes the S-Bahn to the Hbf.
As for what you could find on Trivago and Booking, I'm not surprised. Booking is just a reservation handler and takes a commission (15%, I believe), and Trivago is just a clearing house for the same reservation handlers. I never use booking websites. I've found that the most economical places don't usually use them. If a property does, they might, for example, only offer their most expensive, "deluxe rooms", rooms you probably would not take if you could book directly. In the case of Royal and Lindner, I did find prices on Booking that were close to or the same as from the properties directly, but, whereas breakfast was included in the price at the hotels own site, it was a $20 (for 2 people) add-on on the booking site.