Last two times we have stayed here http://www.evropahotel.cz/en half way down in Wenceslas Square.
Handy for sight seeing.
Its about £60 a night b+b for double room with bath/toilet, cheaper if you don't mind sharing a toilet.
It was like stepping back in time, very art nouveau.
It also had secure parking for the bike which was behind the hotel with locked gates.
Hotel Seven days ... really nice hotel, 2 minutes walk from the top of Wenceslas square, and underground extremely secure parking for the bike ( electric roller shutter door )