When my wife and I went a few years ago, we stayed here :
http://www.987praguehotel.com/en/
It is a bit of a walk to the old town, but very close the train station. The hotel itself didn't have a lot of amenities, but we weren't bothered as we'd prefer to be out anyway. But it was clean, modern, and more than adequate.
And, as with many European boutique hotels, they're usually nicely priced compared with some of the branded hotels. But... you compensate for that by being a bit further away. My wife and I like walking though.