Upvote:2
According to Timatic, which is THE authority used by airlines for determining passport, visa & health requirements for travelers, your National ID is an acceptable travel document. Timatic for Netherlands - Turkey
Chances are the call center agent only looked at the general rules which state a passport is required, but the check in agent will be able to reference the full Timatic listing for your nationality - destination pair. But to be ultra safe you could always print out a copy of the Timatic page and take it with you as a back up.
Timatic also goes on to state that Visas are required, but National ID holders can get a Visa on Arrival for 25 Euros.