I think that those in charge of the game are focused upon money, but they also recognise that they can't just get away with anything they want. They can do things which are unpopular, but if there's too much noise and visible discontent about a proposed change then the clubs will start to take fright and won't support it - and the EFL and PL are nowhere without the support of the clubs.
For me, the point of the boycott is to generate that 'noise' and visible discontent. Just expressing views on forums etc isn't enough. There has to be something real for the papers to write about, and there has to be something to make the clubs believe that this is a bit more than the usual grumbles. Boycotts aren't easy to achieve, because people love their clubs and it's painful not to be there supporting them. So if the majority of fans join in with a boycott - as happened in this case - that's a real statement. It captures the imagination of the press, generates more noise, and forces the clubs to take notice.
The EFL's hope now will be that last week was it. That people will drift back to the games over the remainder of the competition, and by the time they come to time to make the decision about B Teams entering the lower divisions, the boycott and protests will be largely forgotten. They will be able to say that, generally speaking, after some initial concerns by a minority, B Teams have been accepted by fans, and that the majority will welcome this exciting opportunity to see their clubs play against the future stars within the B Teams of major clubs, on a regular basis.
It's really in our hands.