Maybe it is a cliche but not far off when they call Whole Foods Market "Whole Paycheck" but I still shop there because they make every effort to provide quality organic product from produce to cheese, deli to bakery.
Perhaps the key is to shop smart. First, one many items they are competitive with Lunds and Byerly's but that is not saying much because those places can be a bit overpriced. But look for departments like cheese and bakery to go head to head with the quality family markets. Second, Whole Foods has a generic brand that they call, I think, Four Seasons and with that they are competitive. And selectively, I think there are values to be had at Whole Foods. For instance, I found organic maple syrup in fancy modeled tins for Christmas gifts for less than $9.
Make this your measure of shopping success: The secret to shopping at Whole Foods is to leave with a small bag of really special items, if you've gone a purchased a trunk full of groceries, you've probably paid way too much.