For now anyways. I doubt many people with iPads will buy Kindles in the future and Apple's eReader will scale far beyond the kindle because it offers so much more. It will be interesting to see what happens when the Android tablets roll out.
A year from now there will be 2-3 times as many iPads in circulation as there are Kindles. 2 years, way more. Most of these people obviously will not have prior Kindle accounts and they will buy via iBooks rather than a third party app. The size of the pie is increasing, Kindle's slice can't keep pace.
I have my doubts on people preferring iBooks. Amazon.com is a much better place to shop, and as long as I have any other type of machine, the kindle books are more flexible for me.