I am quite happy with Czech Airlines. I use them a few times each year. They are usually on time - I was delayed only a few times due to bad weather. Their ticket prices are very reasonable. Last year they were giving a hot food on flights from LHR to PRG but this year it is just a slice of ham, salad, slice of cheese, roll and some drink.
The only problem I had with them over the years was at London Heathrow when I was checking in and I had just a hand luggage. Czech Airlines use Air France checking and the girl from Air France told me that there is no special desk for people with hand luggage (even that I used it a few times before). I asked her if she was sure and she nodded. I had to spend 40 minutes in the queue just to be told at the end by another checking staff that I did not have to stay in the queue. I told him that I was told by their staff to wait. He called the girl over and asked her why she told me to wait in the queue. She just looked at me and said that she does not remember and walked away! I could not believe it!
The check-in in Prague is straight forward. CSA has special desks just for CSA passengers. It means that you don't have to wait a long time to be checked in.