If that were true, if Ferrari had the FIA in their pocket, then I would think that the various changes in the regs (e.g., the point system) to make it harder for MS to win championships would never have happened. Or MS wouldn't have been penalized (or not as heavily) for the Rascasse incident. Or the $1million fine for the 2002 Austria GP podium shenanigans, the second largest fine in F1 history after the $5million for the Turkey GP organizers. Or the ridiculously low $50,000 McLaren fine and loss of 10 points in the constructors’ championship for a missing seal on an electronic control unit after MH won the 2000 Austrian GP. However, Mika kept the race win. Give it up already - it goes both ways, as it should.
The incidents you mentioned are not comparable. Those incidents were so obvious there was no choice but to punish them. The reason they were punished were motivated by commerce. It certainly did not look good for the sport to see Michael Schumacher being gifted a win in such a manner or Schumacher's latest cheating incident. McLaren were fined $50,000 for nothing. No rule existed so whether the fine was $5 or $5,000,000 it was still wrong. Furthermore, the authorities had nothing left to hit McLaren with: all the team's constructors points had already been taken away.
Finally, it's not just McLaren fans complaining about matters in Formula One, other people have mentioned how personal and underhand the matter has become. For instance, why did the Italian police turn up outside the McLaren motorhome immediately before qualifying.
Ayrton Senna: WDC 1988,
1989, 1990, 1991
McLaren: WCC 1974, 1984, 1985, 1988, 1989, 1990, 1991, 1998,
1999, 2007McLaren: WDC 1974, 1976, 1984, 1985, 1986, 1988, 1989, 1990, 1991, 1998, 1999, 2008
Le coeur a ses raisons que la raison ne connaît point. 
