Jose's got it wrong here.
With Lukaku, Its not as if the crowd planned to groan. It was a natural and spontaneous reaction to seeing a player give up on chasing the ball. There's nothing wrong with that.
With the Rashford sub, its clear that in recent games, the United supporters were getting frustrated about the style of football and lack of attacking impetus. They wanted to see a more attacking approach, but when Jose switched like-for-like, it was like he wasn't going to go harder for the win.. He may not have intended this, but that was probably the immediate reaction from the fans.
The problem with Jose is that he expects unconditional backing from the fans, like fergie had. But he forgets that fergie didn't have this unconditional backing until many years after his appointment. If I'm not wrong, fergie had been booed on several occasions during his first few seasons. It took many years for fergie to earn the unconditional trust of the supporters. Its not fair for Jose to expect this immediately from the fans.
Jose needs to remember that he still has it all to prove, a capital one cup and europa league is not enough. Not too long ago, most United fans disliked him and mocked him frequently. Until he earns that trust, he has no right to criticize the fans.