OK, firstly I'm not sure how ye all descended into a debate about mobile phones and mileage expenses when the OP's question was about the PAYE tax credit!
But to answer the OP's question, the reasoning behind this rule is that a proprietary director is effectively self employed. Generally they have opted to trade via a limited company, in order to enjoy the benefits of 1) limited liability, and 2) the lower rate of corporation tax, compared to the marginal rate of income tax. They are able to dictate the terms of their relationship with the company, decide when and how much salary (and, yes expenses, perks etc...) they draw from the company. Seems pretty reasonable to me.
And as regards it being another way to penalise entrepreneurs, it actually only serves to level the field between a sole trader and a proprietary director, as a sole trader is not entitled to a PAYE tax credit either (nor do they have the option, in the event that they are fortunate enough to make a decent profit, to choose how much to have taxed as a salary and how much to shelter in the company at a rate of 12.5%).