I checked back with Intellichoice to see if they had more details on their study. Indeed they have some more details but it's hard to interpret.

http://www.intellichoice.com/press/Hybrid-Survey-2006

If I am understanding they took all or most vehicles from a given class and came up with a "5yr Expected Cost". They also came up with a "5yr Actual Cost" for each hybrid. If the hybrids actual cost is lower than the expected cost that means the hybrid is a greater value.

"For the survey, 2006 model year hybrids were analyzed for their Total Cost of Ownership over a five-year or 70,000-mile period. The five-year expected Cost of Ownership for each hybrid vehicle is based on the average cost of all vehicles in each class." - Intellichoice

I wish they would provide more detail than this, including the Total Cost of ownership of all of the vehicles used to create the expected cost. This sure doesn't look like a straight comparison between Hybrid and Non-hybrid by model. They say this info will be available in late January, but I can't find it anywhere.

Doesn't appear they factored in the Alternative Minimum Tax, or Zero Tax issues either, but who can tell.