Apparently Whole Foods' Allegro Coffee does pay a fair price, although I haven't been able to figure out what makes it not fair trade.
The following article from BusinessWire (which I found via Lexis-Nexis) talks about the prices Allegro pays growers:
Business Wire
January 9, 2003, Thursday
Allegro Sets Pace for Sustainable Coffee Business Practices; Coffee Roaster Reports Audit Results of Green Coffee Prices
[excerpt]Allegro is committed to working directly with farmers to guarantee that farmers receive a healthy profit in exchange for a high-quality product. Ernst & Young reported that between January 1 and June 30, 2002, Allegro purchased 1.6 million pounds of sustainably grown and certified organic green coffee combined, and the weighted average price it paid was $ 1.64 per pound including transportation, import fees and taxes. Allegro purchased approximately 499,000 pounds of certified organic coffee and paid a weighted average price of $ 1.63 per pound. The average fair trade price reported by TransFair USA, headquartered in Oakland, Calif., is $ 1.26 per pound for specialty coffee and $ 1.41 for certified organic coffee. The "C" price, or commodity price per pound for coffee is currently about $ 0.62, according to the New York Board of Trade.[end of excerpt]
TransFairUSA, "the only third-party certifier of Fair Trade products in the United States," doesn't list any other standards on their website besides the price paid to the grower. The website www.coffeereview.com says that fair trade certification is granted only to collectives. (I don't know anything about Coffee Review, and TransFairUSA doesn't quite confirm this. They say "Fair Trade guarantees farmers a set minimum price for their coffee and links farmer-run cooperatives directly with US importers.") Allegro's suppliers are not all cooperatives, so maybe that's why they're not considered fair trade. Just a guess. They describe their farmers here: http://www.allegrocoffee.com/page.php/id/45.
Also, an article in the San Antonio Express News (January 10, 2004, "San Antonio Coffee Drinkers Pay Premium for 'Fair Trade,' Social Conscience") writes "Some, like Whole Food's subsidiary Allegro Coffee, say TransFair sometimes puts quality second to the cause." So possibly the decision not to pursue the fair trade label has to do with this gripe.