I have had that happen to me once at Schiphol, coming from Hong Kong (haven't noticed any special attention coming from Turkey earlier this year). I don't have any direct evidence that it is the only reason but I do have an explanation. The thing is that ditching your passport is not unheard of as a strategy to make yourself more difficult to remove and pretending to have another citizenship can even give you a fighting chance at getting into the asylum system without being a bona fide refugee (protection officers are not dumb and language and other details can betray you but I have personally encountered people who did this, successfully or not).
Removing someone who does not have a passport typically requires the cooperation of the country of origin and that country must be deemed safe. So if you manage to pass yourself as coming from an uncooperative or dangerous country, you might be able to fend off a quick removal process and hope to ride out detention or find some way to remain in the country legally or illegally. By contrast, if you are refused entry with a passport in hand, you will probably never leave the airport grounds and can be sent back in a matter of days, if not hours (in the EU, you have a right to appeal the decision to refuse entry and can also try to apply for asylum, but there are expedited procedures for blatantly unfounded applications and/or appeals).
By checking people's passports straight out of the airplane, you know where each traveller comes from and it's therefore easier to send them back and to know which airline to hold responsible, if it turns out that a passenger doesn't have the necessary visa (including a transit visa) or tries something like lying about where they come from. This becomes much more difficult once the passengers mix with each other in the arrival hall before approaching the main passport control area. Some countries are also thinking about using cameras for the same purpose (i.e. matching an uncooperative person to an incoming flight and, implicitly, country of origin).
Also, as noted in several comments, citizens from some countries (not Hong Kong or Turkey, though) require a visa even if they only want to transit in the Schengen area (or some specific countries in the Schengen area). This obligation is mostly meant to be enforced by airlines but double-checking might be a way to put pressure on them to check their passengers properly.
Finally, both Germany and the Netherlands are known to require “Advanced Passenger Information” for incoming flights so the police might have a “hit” for one of the names on the flight manifest and be looking for a specific person (could be someone with an open warrant but there are also alerts for missing persons, etc.).