At that time of night, the 119 bus leaves the airport every ten minutes until 23:43. So if your flight lands around 23:00, the chances are that you'll still make a 119 bus. It goes directly to Nadrazi Veleslavin where you'll connect with the metro to the city centre. Get off at Mustek for Wenceslaus Square. It takes 33 minutes and costs 32czk.
If you miss the last 119, then the 510 night bus starts at 23:52 and runs every 30 minutes. It takes 45 minutes to get to the centre. Stepanska is the closest stop for Wenceslaus Square (550m, about 6 minutes walk). It costs 32czk.
However, the 510 is a fairly arduous undertaking. It's a long and winding route that visits every hole in the hedge, so if you can afford to take a taxi it might be worth doing that instead. It will get your to your bed faster and with less figuring out on the way. However, if can you land in time to get a 119, I'd do that and then spend the 600czk that you save on something more enjoyable than a taxi ride.