We just came back from a 5-night stay at Casa Treat for our honeymoon.
It's a lovely pied-à-terre in the Mission district. It's sunny, clean, beautifully decorated, with all the ameneties you need and full of thoughtful touches (a binder with information/recommendations, coffee, plasters, sparkling water, we even had a bottle of sparkling wine to congratulate us!).
It's very well located, close to a Bart station and Muni transit. There's great coffee shops, cool restaurants, beautiful murals and a lot of little shops around. People are nice and we felt safe in the neighborhood.
We're really happy to have found this place and to have stayed there for our honeymoon.
P-S: Don't forget to bring your slippers because the floor can be a bit cold for bare feet.