There's a hell of a lot of power vested in the executive branch especially in the DOJ to really mess with companies and the real protection against it's misuse was the agreement that the President didn't directly instruct and control who the DOJ actually indicted. It used to be a notable event when a president even appeared to hint that he was encouraging investigations (not even indictments) into specific companies now we've got a president explicitly demanding the DOJ indict specific people and find any reason to do so, see Comey and Letitia James's recent indictments.
And, of course, since businesses are fundamentally in competition, that puts them in an interesting position: even if it's a net negative for the entire industry to capitulate to the bullying tactics of the executive branch, you can get a leg up on your competition by having one fewer giant complicated court case to worry about (even if the case is guaranteed to lose, it still costs money to defend it).
Yes, there's a lot of pressure to stay on his good side, even if the charges are bogus and eventually beaten or just ends in a pay-off like many cases the process is still damaging/costly and there's large incentives to pre-comply. Look at Apple's little gift plaque for an example of that, not really a bribe unless more laws are broken but a nice little ego stroke none the less.
