Tom Brady has one of the most team-friendly contracts in the NFL due to a restructured contract in 2013 and a subsequent extension.
Before the renegotiation, Brady was scheduled to make $30 million through a couple of high salaries. After the renegotiation, that number became $33 million, consisting of a $30 million signing bonus (the last deferred payment of which was paid in February to the tune of $5 million) and salaries of $1 million for 2013 and $2 million for 2014. Thus, the Patriots got better cap flexibility due to the prorated bonus while Brady received significantly better cash flow and an extra $3 million to boot.
The deal added an extension with "out years" in 2015, 2016 and 2017 at salaries of $7 million, $8 million and $9 million respectively, which are low for a quarterback of Brady's caliber.
At the end of last season, there was a renegotiation to bring the salaries for those years up by $1 million per season.
Brady is earning roughly $10 million per year below his market value.