That said, adding in those factors often makes Silicon Valley come out even worse. I've visited it quite a bit and it is not nicer enough to account for cost-of-living difference, unless you simply can not stand to live somewhere with less than perfect weather. But I think that's special to the Valley.
It's interesting that you bring this up. In the case of food, at least, lower COL areas (which are typically more rural) have access to something far better than any store - farmer's markets and actual farms.
There's a "cheap basics" grocery store in a 5 minute walk, a farmer's market in a 10 minute walk, and a Whole Foods in a 15 minute drive.
I don't really care about organic produce, but that flash pasteurized OJ at Whole Foods is really worth the extra $2.
It's a nice area for certain, but it makes me wonder about myself when I'm wearing a parka and everybody else is walking around with a scarf or light jacket.
Parking is a big difference though. You can rent an apartment in the Midwest for what it takes to park a car in some major cities. Not to mention higher gas and insurance.
I live in Cincinnati with one of the most top 10 most expensive airports in the country (CVG). I also spend a lot of time traveling and searching for flights.
One strategy I've used to avoid this is booking Kayak-style "hacker fare" for a domestic ticket to a hub like LAX/ATL/etc. with an international flight out from the hub, then a return ticket from destination to home (with connections of course).
It doesn't sound like it'd be that significant, but it made a recent trip to New Zealand & Australia about 40% cheaper, though it does take some extra effort.
When I put everything on a spreadsheet, the lower housing costs in other parts of the country didn't sufficiently make up for the drastically lower salaries. YMMV, but I encourage everyone to very carefully do the math before making these kinds of decisions.
(I do think that SF may be a special case, since it's SO expensive, but even then it's worth doing the math.)