Several side by side blind comparisons of the same beer in both formats have been done. It's very hard to tell which vessel the beer came from and it almost seems as if the can does a better job of retaining freshness and carbonation. With that being said, the biggest argument against cans has always been that they seem to leave a metallic taste behind, thereby tainting the flavor. Today, this argument is not valid as all cans these days are lined with a water-based polymer that prevents the contents from actually coming in contact with the actual can. In fact this is a must, as the aluminum cans we use today are so thin that the beer would quickly eat right through them. As for the contact with the top of the can when being consumed, if this really bothers you that much simply pour the beer out into a glass. We also shouldn't forget that draft beer usually comes from an aluminum keg, right?
Two other huge benefits that cans provide are that they pretty much completely block out UV light and allow almost no oxygen in after being sealed. The same can not be said about bottles. Light and oxygen are two of beer's biggest enemies as they quickly cause the beer to lose it's flavor and freshness. So cans actually preserve their contents and protect them better than bottles.
Other pros for cans: they fit in a cooler better, they are stackable, they won't shatter when dropped, they are more conducive to outdoor activities, and they don't take up as much room in the recycle bucket. It almost seems as if cans were made for the warm weather. They are perfect for the beach, the pool, or for hiking. Tailgating with cans is safer as you don't have to worry about stepping on broken glass.
So the evidence is quite clear: cans don't deserve the stigma that still seems to follow them around. They are just more practical. Even though you most likely won't see your favorite bottle conditioned cellar worthy Belgian ale or barrel aged stout in a can, it is pretty safe to say that cans just make more sense for most companies and consumers.