I stayed in Prague for my 21st Birthday. The 987 Design Hotel was on offer through last minute.com which was the main reason we chose it.
It is fairly central to the main parts of the city (within walking distance) but there is also a metro station opposite which is relatively cheap and easy to use.
The layout of the room was very modern and the shower was brilliant- the only thing I would have liked was a bath but this is not a problem.
Don't be out off with the location so close to the station as it will not affect your stay in the hotel.