It might sound simple, but won't tunnels lower the strength of the runways (I presume that's where you would put them)? Strengthening that would create an expensive solution to a basic communication problem. That's like saying instead of 4 way stops, we elevate the two intersecting roads to avoid collision, just because someone may have ran the stop sign.

Also, ground vehicles typically need to be on the ground for a reason. Why seperate them?