I think being taxed 59% is outrageous, even as a benefit in kind your tax rate is lower. I am surprised Gordon Brown et al havent found a way of taxing staff travel for you to really get his pound of flesh.
That means 59% of the amount (of allowances) is taxed, not that it is taxed at 59%. It is taxed at whatever is the appropriate rate, depending on total salary etc, probably 20%. The non taxable element of allowances are deemed to be expenses, not salary. (Although perhaps by eating somewhere cheaper, it is possible to make a profit on a meal allowance for example)
Why staff travel isn't taxable has already been discussed.