Even the smallest regional commuter planes now come as jet. I recently had the pleasure to fly with a Dash 8 Q300. Did you know that the fuel consumption per passenger kilometer is considerably lower than on a comparable jet plane?
Also, as these planes cruise at a lower altitude, I assume that the additional effect of emissions at high altitude will be lower.
Propeller planes have two disadvantages: Their maximum speed is only about 500 km /hr as opposed to 900 km / hr for jets. However, for anything under a distance of 1,5 hrs this amounts to only about 10% more travel time. The other disadvantage is the higher level of cabin noise. Guess what: with the latest in Noise cancelling headphones, this does not matter.