I have a GE Profile glass top and this is what I learned.
I believe the reasoning behind the water canner and the glass top stove is that there are ridges on the bottom of the canner, making contact with the stove more difficult.
That being said, a water canner can be pretty heavy, so I suppose there is also a weight factor to consider. I had mine going without any problem. And even taking the ridges on the bottom into account, if your water is at a full rolling boil, you should be good to go with canning.
If you are concerned that the size of the canner is bigger than the element, I called GE customer service and they said that's not a problem. It would be a problem if you had a large pot that was wider than the burner with hot fat or if you were making something exceedingly hot like candy, but she said the temperature of water will not hurt the stove top.
If you are interested in a pressure canner, Presto makes one that is fine to use on the glass top stove. Another advantage to the pressure canner is that you only use a couple inches of water so it's much lighter, not to mention shorter canning times and much less heat/humidity released into your kitchen. A pressure canner can also double as a boiling water bath if necessary.