There's a few different ways to answer this question, but the simplest answer is because the Supreme Court has allowed for broad presidential power in regards to pardons. Their deference is probably because the power to pardon is written into the Constitution in pretty clear terms: "and he shall have Power to grant Reprieves and Pardons for Offenses against the United States, except in Cases of Impeachment." Note that the president has the power to pardon those who committed "offenses against the United States," rather than say, the power to pardon those convicted.