I am an extension provider working with Enterprise, and wanted to share some of the reasons that are behind the decision to charge more for an Enterprise version extension.
To be able to officially offer Enterprise version extensions on Magento Connect (and to access the testing versions), you need to be a Magento partner. This incurs a yearly fee with an entry level of $10.000 per year. There are a couple of different ways to look at how to absorb this cost, and it's not always fair to raise the price of Community extensions (though it's a far bigger market) simply to be able to officially offer an Enterprise version extension. Enterprise is a fairly small market, so the cost of entering and serving this market is spread across fewer people.
From a technical standpoint there are differences - Philwinkle already mentioned a few. I would also add to that list the range of custom totals that come out of the Enterprise features (like points, credit to account, etc), staging sites and restrictions, additional promotional capabilities - depending on what an extension does, these all need to be considered. Additionally, Enterprise releases never seem to follow Community releases one to one - so the codebase might be fairly similar, but it does not match.
In my view, supporting a given version of Magento (Community or Enterprise) means that you need to test the extension against this version and be prepared to answer/troubleshoot all support questions that may arise. Any quality extension will always be tested extensively on all versions that it officially supports.
In terms of our own process, once we have made sure that an extension works on Enterprise, and supports the Enterprise features you would expect, this extra effort is oncharged in the way of a higher Enterprise extension price (a cost that's not always fair to pass onto Community customers). Technically you might be able to install Community versions of some extensions on Enterprise, however this would not be officially supported and does not come with the guarantees of having being tested and compatible with all features.