The alternative to having an AMI booted from an EBS partition is to use the non-persistant instance store instead. This is slightly similar to when you boot an operating system with a Live CD, where the Live CD would represent the AMI in the S3 bucket, which is immutable. In both cases you lose everything when the OS is shut down.
Keep in mind that AMIs with EBS-root instances have been supported only since December 2009. This could be one reason why there are still more public and community AMIs that use the instance store instead of EBS for the root partition. On the other hand, one drawback inherent to EBS roots is that you pay for the EBS storage and I/O traffic, while the use of the instance store was free. However this cost is often not considerable, but will depend on the nature of your application. Also note that you will continue to pay for the storage even when the instance is stopped.
In addition, I think this article from the FAQ confirms the above, and describes one scenario where the instance store is preferred:
What is the difference between using the local instance store and Amazon Elastic Block storage (Amazon EBS) for the root device?
When you launch your Amazon EC2 instances you have the ability to store your root device data on Amazon EBS or the local instance store. By using Amazon EBS, data on the root device will persist independently from the lifetime of the instance. This enables you to stop and restart the instance at a subsequent time, which similar to shutting down your laptop and restarting it when you need it again.
Alternatively, the local instance store only persists during the life of the instance. This is an inexpensive way to launch instances where data is not stored to the root device. For example, some customers use this option to run large web sites where each instance is a clone to handle web traffic.