Curt Gentry in J. Edgar Hoover, the Man and his Secrets, along with several other scholars before and since have noted the FBI's use of illegal wiretaps and "black bag" operations likely benefited multiple Presidental administrations in that Hoover used information on political opponents of sitting Presidents to curry favor. There is some evidence to support these claims.

Further, so the argument goes, Nixon was keen for Hoover to do the same for him and he was more than well aware of Hoover's activities under Eisenhower and the Kennedy's use of any number of nefarious methods in the 1960 election for which he bore a powerful grudge. Hoover demurred. The story is that Nixon's aides convinced him to fire Hoover and install a new director that would play ball. Hoover was called to the oval office for a one on one meeting, where Nixon was supposed to fire him and ask for his resignation. At the conclusion of the meeting Nixon walked out with Hoover, told him he was doing a great job and to keep up the good work and that was that. Nixon's aides were stunned and Nixon never revealed what happened, supposedly that is also one of the "missing" parts of the Nixon tapes.

The real basis of Hoover's caution was more about cementing his legacy. The FBI, NSA, CIA and military intelligence were all up to no good in the 60s and 70s (hence the Church Committee) and Hoover didn't want to risk tarnishing his legacy if they got busted. His grip on power was ebbing and he was nearing the end of his life and knew it. It is hard to know for certain though, as he didn't exactly tell anyone who would repeat it (Tolson certainly knew). In any case, his refusal to play ball with Nixon led to the White House plumbers...and the rest is history.