I tend to agree - the points penalty punishes the fans more than it does the management.
That said, there needs to be a punishment of some sort for financial mismanagement otherwise unscrupulous clubs would buy players they couldn't afford to try and gain an advantage over clubs who manage their finances more prudently.
However, I'm not sure if the Football League have the jurisdiction to financially penalise the individuals running the clubs as I guess it's not strictly speaking "illegal" to over commit a company's spending which is why they resort to the 'easy option' of penalising the fans.
Dunno.