Two Reasons:
1. Hospitals get paid something like 100k per year by the government to train each resident. But most fellowships are not funded by medicaire, so they get paid less.
2. Fellows can theoretically moonlight to feed their family.
Yeah, most fellowships are paid for mainly by the faculty, either through their clinical or grant revenue. Departments give little, if any, and there is no govt funding, as has been stated.
Of course, most fellowships do not allow, or strongly discourage, moonlighting. After all, you only have 1-2 yrs to "master" your subspecialty.
The high-earning subspecialties (plastics and retina) also know you'll recoup any salary losses through an increase in future earnings. There's no real motivation to pay you more.
In short, if you want to pursue a fellowship, don't focus on the 1-2 yr salary. If you land one of the better-paying fellowships, good for you. If you don't... Moonlight if you can. Take out loans, if you need to support your family (though the current state of the economy may restrict you to running up credit card debt). Lower your standard of living for a time. But, follow your passion. You'll make enough to be comfortable in the long run, and you'll enjoy doing it.
I've taken out 20K in loans this year, but I'm not batting an eyelash. I'm doing what I love.
😀