Mrs. OJ and I stayed at the Palace Hotel on our honeymoon (1971) and a few other times in subsequent visits -- most recently for 40th anniversary. They might give you a special deal if you tell them you're honeymooning -- we were given a small suite (bedroom and separate sitting room) for the price of a regular room ($26 in '71). Also, check their website for special package deals -- some are especially good bargains.
As for the hotel itself, it's a grand old, historic hotel in the best sense of GRAND. Elegant and posh, the rooms are quite comfortable and add to the romantic atmosphere. By all means treat yourself to brunch in the stunning Garden Court dining room. It will add to memories you'll treasure forever!
It's right off Market Street, tucked between Union Square and the Embarcadero. If you want art and culture, the San Francisco MOMA is just down the block.
Edited: 4:37 pm, February 20, 2013