First off, the primary problems are that people say they can taste the metal and it looks less classy or craft. As far as taste goes these days the cans are all heavily lined with a polymer (basically a high tech plastic layer) that makes it so there's no leaching of the metallic flavor. Now you might get some of the flavor if you are drinking directly out of the can, but you should be pouring all craft beer into a glass anyway (this helps release more of the aroma and allows the beer to breathe). Probably the biggest issue with the can is that people consider it to be of lower quality. We are so used to having national big brews in cans that we assume anything that comes in a can is not as good as a bottle (which traditionally held importers that we assume are higher quality). This is similar to the issue people have with boxed wine. The airtight pouch inside a box of wine is actually the best way to store a good vino.
Other benefits are that you can take it to sports games, tailgate parks and other venues that might frown on broken glass. Cans are universally more acceptable than other types of containers. Also there is a solid environmental story. Cans are one of the most recyclable materials we use. According to The Aluminum Association, creating an aluminum can out of recycled materials requires only 5 percent as much energy as creating a brand new can from bauxite ore. This is a more efficient process than most glass.
Drawbacks for breweries with cans are pretty serious. All container designs that are going to hold beer or any alcoholic beverage have to be approved by the ATF (alcohol tobacco and firearms) so getting each design can be costly and time intensive. They have to have specific information on them about the individual beer. Printed cans have higher costs and higher minimums than labels for bottles. I am sure every home brewer has gotten a pack of Avery labels and printed them out at Kinkos to put on their beer. A brewer can do this on a much larger scale, therefore getting it for way cheap. Cans on the other hand have much larger minimum orders because of what's needed for custom printing.
Same can above right and left with a different circular sticker.
Sun King does sort of a mash up. Their specialty beers have small stickers on the beer cans indicating what brew is inside. This lets them do large runs of Reserve cans and Standard cans with general Sun King information and then add the sticker to get everything else that the ATF would require.
Right now we are seeing more and more breweries using cans. Locally Sun King and Tin Man have embraced the change and nationally we are seeing a lot of cans out of Sixpoints and many others. As the average craft drinker gets better educated I see this trend increasing. I believe we can all put old biases aside and embrace what is better for the brew and for the planet. God I sound like Al Gore...
Special thanks to Alex Linz from Unisource Worldwide and Ron Smith and his Masters in Beer Appreciation class.