I think, Venice is still the only city literally charging an entrance fee. They do that, because they got more tourists, than the city could handle. But I think what you have heard might be about tourist taxes. Many cities charge those per night. But you won’t notice it directly, it’s just that, if you’re staying in a hotel, they’ll automatically add it to the price of the room.

I second Prague. It’s beautiful and worth it whether you come for the history or the culture or the atmosphere.