Czech Airlines provides an efficient service. I usually only change planes in Amsterdam, so I don't know how their check-in looks there, but the ground personnel is always very polite and helpful.

The flight to Prague is only about 1 hour, so it is surprising that you get a full breakfast, lunch or dinner (depending on the time of your flight). They have code-sharing with KLM on this route, but the service and food is incomparable. On the Dutch carrier you only get a dry sandwich.

The duty-free is quite cheap and they always have all the products that are in the catalogue. Another plus is that they are very benevolent with excess luggage and usually don't care whether it surpasses the limits.

I definitely recommend Czech airlines on this and other routes.