You'll probably find that's true of most if not all places, you get "local" prices and "tourist" prices. Part and parcel of travelling to exotic locales.
However, lot of taxis I've been in around the world have a tariff board, so you can sort of hazard a guess at how much our trip should be...
A bit crap, but it's travelling for ya... about 7 years ago
Negotiate the price before you use taxi or use a reputable company (e.g. in Prague AAA radiotaxi (note this name carefully), Profi Taxi, City Taxi). all legitimate taxis are painted yellow.
Always insist on having the taxi-meter turned on and ask for a receipt once you reach your destination, it should have driver's name, address and tax identification number included. But watch out, some of the meters have been tampered with to go more quickly.
There's an information desk at most taxi stands in the city, with prices to popular destinations. But a legal loophole allows some companies renting the taxi stands (specifically around Old Town square) to charge VERY high prices. The most infamous company is AAA Taxis... their name deliberately resembling the legitimate "AAA Radiotaxi Praha", however AAA Taxi cabs charge up to four times more.
But try to keep some perspective on this..... you'll pay a few Euros more for a taxi ride, but it's not like they've stolen your life savings.... just one of those things abiut travel, don't let it spoil your trip to this very lovely city, and don't let it colour your opinion of Czechs - mostly they're friendly and helpful people. about 7 years ago