Since inception they've benefitted from lower capital and mortgage insurance costs due to their implicit government backing. In return, they've accepted substantial oversight from the government in regards to their loan acceptance standards.
The 2008 rescue and then QE where the Fed bought Agency debt by the billions made the implicit government guarantee very, very real.
When Fannie and Feddie went insolvent, Congress and the Obama administration as the rescuers had the opportunity to completely wipe out the public shareholders and take over the companies. This is what should have been done.
Instead, we now have zombie public companies whose profits are siphoned off through political agreements instead of explicit contracts open to public scrutiny.