So why is the use of aluminum so discouraged? When I bought my stuff, I went by Charlie Papazian's recommendations and he says not to use one.
Some years back there was a scare that aluminum cookware might be responsible for Alzheimer's Disease, so that might have been it.
Aluminum transfers heat well, is lightweight and inexpensive, so in theory it's a good metal for cooking. By contrast, stainless steel doesn't transfer heat nearly as well, so stainless pots are more prone to producing hot spots. That's why upscale stainless steel pots have copper bottoms, since copper transfers heat extremely well.
The drawbacks of aluminum are that most aluminum pots are fairly soft, so are vulnerable to scratching and denting. They can also be depassivated or pitted if you use particularly harsh cleansers on them. Finally, aluminum also isn't good for cold-side usage because long-term exposure to acidic solutions (i.e., beer, which has ~ pH 3.2 - 4.8, or wort, which has pH 5.6 or lower) leach metal ions into your beer, giving metallic off-flavors.
Stainless is preferred in commercial breweries because of its durability and ease of cleaning, but there's no reason you can't use aluminum or even copper for your hot side operations.