Do professional pilots have to show their passports every single time when flying back & forth between the same airports?
Pilots (and aircrew) usually go through an expedited security screening, usually separate from passengers, in order to reduce wait times. 

For example, US TSA has a program called the Known Crewmember Program that allows pilots and crew members to bypass normal (passenger) security line.

Pilots (and aircrew) have to show the documents as required by the local authorities. Usually, this will be the passport/visa or General Deceleration. This varies from country to country.