Whole Foods to us is a great place. It's also not a once a week store. Mainly given the distance to drive but for some of the reasons mentioned about price. When we lived in KCMO, Overland Park was 15-20 minutes to drive and gas was also 2.00 a gallon so once a week wasn't an issue. But now and the fact it's twice as far, it'll probably work out to be an every other week store.
We usually split the purchases between 2-4 different stores anyhow. Trying to get the best quality for the price. There are some things that we feel are necessities and if they happen to be more expensive that the "price you have to pay".
Whole Foods offers products that are not readily available at our Ukrop's, Kroger, Costco or on the low side Sam's. Their house brand (365) is also very cost effective and the quality is quite high.
So I guess I would have to say we use them for the more culinary items. Vinegars, oils, spices, some meats (they are the only store that sells a skin-on butterfly boneless breast of chicken and a Cap-on sirloin), sodas (again the house brand being reformulated with pure cane sugar), Cheeses and several produce selections.
I also often question the added cost for things because they are organic, healthier, whatever. Yet if you look back through time, health always costs more. Most folks entrenched and around the survival point don't often have time to think of or even prioritize about healthy food purchases. yet there are always exceptions so don't jump on that statement.
I guess it is what it is and until more things change than I believe are possible (this is the real world and ain't Star Trek TNG or......) it is what it is and we do what we can when we can.