depends on the plastic the water container is made with. If you have #1 plastic, chemically speaking, you should be fine. #2 plastic, there is some debate on, but more people fall on the side of it's OK to use. Any other types of plastics (especially #7) leach a chemical called BPA into any acidic environment (including beer). This chemical can cause some health issues.
Aside from the chemical argument, many folks have a problem with using the water container because the user doesn't really own it - you are technically leasing it from wherever you acquired it, with the implicit agreement that you will bring it back, and get a new container. That argument doesn't hold any water with me as #1 I've paid money for it (albeit a small amount) and #2 the cost of production is much less than what I've paid for it. But I may not struggle with my moral dilemas as much as some.
Other than those areas of concern, mechanically, they will work just fine. They even will fit a standard better bottle topper to hold the airlock. The one reason I don't use them for anything other than cider, however, is that when you use a 5 gallon container (better bottle, carboy, or water jug) for beer, you almost always have trub at the bottom and accounting for volume loss, you usually end up with about 4.5 gallons for bottling. I like to get more than that from my batches.