The key difference with a plain old-fashioned orbital rendezvous would seem to be that there'd be limited time to only briefly match velocities and trajectories:
Let's say a vehicle launched from the ground on a suborbital trajectory wants to meet a space tug that had slowed down from LEO for payload handover.
Assuming the tug had slowed to 5 km/s, and the ascender accelerated to exactly that velocity, just under 2/3rds of minimum orbital speed. If either the tug, or the ground-launched vehicle were just 1 second off, the vehicles would be 5 km apart, and you'd have to do the measuring, calculation and navigating to bridge that gap within a few minutes before their trajectories had to diverge again, as the tug would soon have to fire its thrusters to get back into orbit before entering the atmosphere together with the suborbital ascender.
If you were just a millisecond off, it'd be 5 metres, and considering that the relative trajectories were divergent, again there'd be little time to fix it.
I can't find anything on this online. It would seem to be a useful technique as it would lower the delta-v for the vehicle that lifts the payload from the ground to the rendezvous point relative to fully making orbit. (NOTE: Yes, you'd have to get extra fuel to the tug to perform this manoeuver but that's potentially a smaller problem.)
Is it just too hard so no one's ever contemplated trying?
EDIT I: The first answer (now deleted) made before this amendment of the explanation and of the title to make it clearer that the question isn't about planes meeting in the atmosphere was technically correct, aerial re-fueling in the atmosphere is a suborbital rendezvous manoeuver. However, I assume the upper vehicle here is on a trajectory to re-enter orbit either because it's the end of a tether that will spin up by virtue of its momentum or a space tug which would have to fire its engines before entering the atmosphere.
EDIT II: As @bitchaser pointed out below in the comments to the first answer, the slowing down might happen via aerobraking to save fuel, and engines on the tug could be optimized for the purpose of re-injection into orbit.