Unfortunately Binotto is a good person to stabilise a ship and a bad one to navigate it at speed. He locked onto the original goal of "be competitive" without noticing that the goalposts had moved to "try to win the championship". He then failed to meet the promises he made after the Silverstone disaster* (namely that he was going to sort out the strategists and stop them from making such egregious errors, stop blaming implausible factors for not winning races and also stop denying there was a problem when there obviously was at least one problem). All of these were broken in Brazil qualifying**. At that point, the position was untenable.
* - There was a 1-3 (with a small chance of 1-2) on the table, Ferrari got a 1-4 and was extremely lucky it wasn't a 1-7... ...and achieved it with the sort of error that most strategists learn not to do on their first day on the job.
** - I like to think that when Charles Leclerc looked back and saw everyone else was on dry tyres while he was on intermediates, that he also saw Mattia's Ferrari career ending in that moment.
You can't have stability in a team if the guarantee is of failure. Yes, the strategy improved, but the impression was that this came from the drivers fighting to get heard over management (and having better ideas about how to do strategy than either management or the strategy wall, despite both predating their arrival on the team and despite neither driver being hired to do strategy). The impression was that Binotto was outright contributing to that issue being an issue, at least.
Ferrari had patience with Todt because each year was a logical progression. The early years that had no obvious improvement of results, did have improvements in the background, concerning how things were arranged. Problems were solved logically at the point where it made sense to solve them, and once Jean Todt got all the people he wanted (which finally happened in 1997), the gradual improvements were visible from the outside as well. 2nd in 1997, 2nd in 1998 while fighting an arguably stronger championship contender, 1st in 1999 until Schumacher broke his leg and constructors' champion in any case, domination started in 2000. It's easy to be patient with someone who improves every year. Not so easy with someone who has exposed flaws implying they are part of the problem.
Which is unfortunate, because the impression I get is that Mattia is exactly the person you want in charge if your team has an unexpected major setback, or if it is in a weak position. The positivity he is able to build up in those situations is very good and he does have some useful problem-solving skills for teams in such a position. Ferrari improved to the point where it no longer needs Mattia, which is a credit to him, not just a deficit. Daft as it may sound, I wonder if Ferrari and Alfa Romeo would now benefit from swapping bosses. (Mattia can get back to problem-solving a midfield team, where I think he would excel, and I think Frederic Vasseur would be able to mount a title challenge for Ferrari, FIA permitting).