Police may only stop vehicles if there is, at a minimum, reasonable suspicion that an offense has occurred, is occurring, or is about to occur. Vehicle check points may be employed if there is no discrimination of motorist (i.e., the police can't stop all Fords and nothing else, all Hispanics, all BMWs, etc.). The police can waive thru motorist if traffic is backing up, they may employ a scheme-such as checking every 5th car, etc. It seems stopping only motorcycles, with no reasonable suspicion, would be a Consitiutional violation (4th Amendment). I can't see a vehicle check point of "motorcycles only" passing a constitutional test either. Depending on the state, Commercial Motor Vehicles may be stopped for random inspections by law law enforcement officers. This doesn't apply to passenger vehicles.
If you'd like the US Supreme Court case that requires the police to have a reason before stopping a vehicle, Google Delaware v. Prouse. Sorry for replying with such technical mumbo-jumbo.