Well - for starters the lower capitalization costs that only these two companies enjoy means that the firms have to spend less money to back the loans they make and to buy insurance on those amounts. Of course, maybe if this wasn't they case they would have been sheltered from some of the downside.

An example of other benefits:
"Congress exempts embassies, non-profits, and certain other organizations from taxation. For example, Fannie Mae receives a Congressional tax exemption that results in a loss to DC of $450 million annually. "

http://standupfordemocracy.org/commuter_tax.html