Few things:
1. Pros spend a lot of time in aerodynamically significant speeds. Even their climbing speeds can be fast enough to warrant drafting (unlike people like me, where climbing at 6 mph means aero means basically nothing). Pros will regularly climb shorter climbs at 25 mph, and a long climb might be 15-18 mph. A really short climb (1-2 km), at a crucial part of a race, might be closer to 30 mph (I'm thinking the Poggio in Milan San Remo, where guys are going so fast they have to take care in the uphill switchbacks). A slight increase in aero benefits can, over the course of a long race, make a difference.
2. A tall rear wheel helps in high speed descents. It stabilizes the bike. (On the other hand a tall front wheel destabilizes it.) I'll put a taller rear wheel on for a training ride if I figure I'll be going over 45 mph on a descent, especially if the descents are long and on long rides, so that I can relax a bit I do this even if it means adding 250g weight just for the rear wheel.
3. Pros' bikes have to meet a minimum weight (about 15 lbs). If the bike is already light then aero wheels may help the bike meet the weight limit while giving a benefit to the rider (as opposed to steel slugs in the bottom bracket axle which don't do anything to help the rider). Seeing as some of the bikes, stock (i.e. you can go and buy one in a bike shop), weigh around 10-12 lbs, there's a lot of weight to add. Aero wheels, even if they weigh a few hundred grams more, will help make up the extra 2000 grams they might need to add to a "standard" light build of a given frameset.
4. Pros tend to spend a lot of time at a high cruising speed (for you and me - for them it might be "tempo"). Aero wheels help the racer in these steady speeds and additional weight in the rims doesn't really affect the rider/bike unit. You'll see the domestiques, the guys assigned to do the pulling for a long time, outfit their bikes with taller wheels (70-100 mm). You'll see the jumpy climber types using lighter wheels (typically, not always). Sprinters usually use a taller but not the tallest rims, like 60-80 mm, to get aero benefit while (probably) getting a stiffer rim, better handling in dicey situations, and saving a few grams rotating weight.
5. Finally the sponsors like to show off their most expensive wheels
Aluminum wheels may work well on a climb but it's much better to highlight a more expensive carbon wheelset. One year, when Campy introduced a new "high end" aluminum wheelset, some teams had their spare bikes outfitted with those wheels (on top of the team cars) while the team rode the Campy's standard carbon wheels. It's marketing among other things.