Yes, you will never have protected bikeways on every street and road nor even on half of them. Nor do you need that.

The Netherlands essentially has 2 types of general roads; Bicycle Streets and Other. Bicycle Streets are those where motor traffic and bicycles share the road. Speed limits are 18 mph or below and in many cases cars are not allowed to pass bicycle riders. The majority of these are narrow single-lane one-way streets and often with chicanes produced by alternate side parking or other hard elements. I ride on these frequently and they are generally quite safe.

If speed is to be above 18 mph then there will be a separate bikeway either a painted bike lane or a physically separated protected bikeway. If speeds are to be above 25 mph then there will be a protected bikeway (protected by curb, grass, parked cars, etc.).

In addition there are motorways that are, similar to our interstates and highways, for motor vehicles only. There are also numerous bikeways not attached to any motor traffic road.

Applying Dutch CROW standards to NYC: The majority of streets would be limited to 18 MPH, designed to enforce that, and shared by all. Some number of larger streets would have higher speed limits and volumes of traffic along with protected bikeways. And this is actually the direction that NYC is slowly going.