As a pilot, I can tell you that like anyone else, I (we) appreciate when people let us know they enjoyed their flight, or even clap at our landings.
We cannot always avoid turbulence, but I can tell you that we take each and ever landing seriously, despite how routine they may seem. (and to the fella who confused ILS with autoland, even those aircraft equipped with autoland systems, we use it less than 1% of the time)
You tip waiters and hairdressers, you say thank you to soldiers even if they have not have ever seen combat, and thinking back you have probably clapped your hands for some really silly things.... There is nothing wrong with clapping, or expressing your thanks for a job well done to the flight crew.