1997 VW Jetta 2.0 engine cranks but wont start

1997 VW Jetta 2.0 mileage: 40,000. I have never had this problem until now. After driving the car during the day, I tried to start it a few hours later, the engine was cranking, but it wouldn't start. I had the oil changed a few weeks earlier and had them replace the air filter also. I looked under the hood and noticed that the air cleaner cover had not been put on correctly. The roads were very wet that morning so I thought it may have gotten some moisture into the intake. There was some water in the hose that goes from the air cleaner box to the intake. I cleaned it out and reinstalled the cover correctly, but it still wouldn't start. I then checked the distributor cap to see if there was any moisture. It was dry, but there's a lot of carbon on the inside of the cap and the terminals. The rotor is also blackened on the outside. Could this be the problem? Is it possible that the loose cover was the cause?