What is the best way to get from Prague Airport to my hotel in the centre for two of us with 1 suitcase? Can we just catch a taxi or is there any alternative directly at the airport?
Yes Taxi would be best faster and not too costly too
You can take the 119 bus directly to the end of the green line and take that into the center for like a dollar each. Or you can get a taxi!
Bus 119 picks up right in front of the airport. It is only a few dollars and brings you right to the Nadrazi Veleslavin metro station, which runs right thru Old Town. It's very easy to navigate.
You can book a shared shuttle from the airport to your hotel for the equivalent of about £10. (book online) There are also lots of taxis outside the airport and they are pretty cheap - I think I paid about €15 each way.
Going frequently to Prague, I've been using Prague Airport Transfers for about 8 years. They're very reliable, inexpensive, and I've been booking successfully online for the last 4 years. I've often booked a "shared shuttle" service and have been alone in the minivan, or with max. 1 other person. Drivers speak English, if only basic, and are friendly. I've always gotten great local tips from them too.
The 119 bus and metro combo is great, but it's often crowded and jostling luggage on the bus isn't fun. There also may be some stairs or multiple escalator trips going from the bus down to the metro, so that might be an issue for you too. Lastly, the metro stops at midnight (or maybe 1am), so be sure to check that if your plane's arriving late at night. Even so, you can always catch a cab. Apparently AAA is the best, and trustworthy.
But as you only have 1 suitcase....I'd take the bus and metro for sure (just check your arrival time). Cheap, reliable, and you get your first listen of Czech :)