The Center for Neighborhood Technology has an amazing online tool that maps 161,000 American neighborhoods and adds the transportation costs to the housing costs in a given place so you can see how affordable (or not) the far-flung exurbs really are.
In the lefthand map above, the yellow areas show where housing is less than 30 percent of average income and the blue areas show where it's more than 30 percent. On the righthand side, the yellow areas show where housing costs plus transportation costs are less than 45 percent and the blue areas show where that combined measure is more than 45 percent. It's an indirect comparison, but as you can see, a lot of places look cheap when you just look at housing (on the left), and that picture changes when you factor in transportation.
You can play around with the updated affordability index here and read their announcement about the release here.