There are convenient flights into nearby Leon, Guanajuato through Dallas Fort Worth, Houston, Los Angeles and Mexico City.
Transportation from the Bajio airport: As you clear customs, once you've passed the sliding doors, to your left you'll find a booth of authorized taxi cabs. You'll have to pay at the booth, indicating that you wish to go to Guanajuato and giving them the name of your hotel. That should be enough information. The cost should be around 300 pesos (approx. 30 canadian dollars).