Not to get all political or anything, but I always feel a bit conflicted when it comes to whales or whale sharks in captivity and have a hard time supporting aquariums with these exhibits. As divers we have the ability to interact with these creatures in their own habitat, and seeing a whale shark behind a glass plate pales in comparison to having one swim right up to you and show genuine curiosity about you.
I'm a volunteer at the Georgia Aquarium, which is actually its name, as opposed to "Atlanta Aquarium," and I've heard this before. Unfortunately, most people don't understand the origins of the whale sharks here, and what their original fate was.
The great majority of the animals at the aquarium are rescues, and that includes the whale sharks (and the belugas, who were rescued from a small sub-adequate tank in Mexico City). The whale sharks at the aquarium were originally targeted for the dinner table -- the flesh is eaten, the huge liver is processed for its oil, and the fins often end up in shark fin soup, which is also largely responsible for the decimation of over 100,000,000 (yes, that's one hundred million, with an 'M') sharks killed EVERY year. The GA whale sharks were rescues, and now inhabit the largest aquarium tank in the world, at over 6 million gallons.
They not only continue to survive, but as a result of being able to work with them so closely, the marine biologists are learning exponentially more about them than they possibly could in the wild, which means being in a much better position to help perpetuation of the species in the wild.
If any of you do visit the aquarium, I would recommend you spend a couple of extra dollars, and do the 'behind the scenes' tour. Especially as divers, you'll appreciate how well controlled and supervised all the animals are at this facility, how well the environments are monitored, how often the water is tested (many, many times each day, with state-of-the-art analytics), and you *will* come away with a new appreciation for the benefits of this flavor of facility that go well beyond a typical "fish show."
In addition, all the volunteers (floor walkers, divers, hosts, etc.) are extremely well trained on each of the exhibits, and the resident animals, from an historical, current status, and future prognosis, of each the species. They are tasked with educating all the visitors on the successes, plights, and requirements of the species in each of the exhibits, so the visit experience can be appreciated at a much deeper level.
So, while I understand the hesitation some people have about large captive species, please reserve any judgements until you've had the opportunity to experience it for yourself.