A targeted tax exemption is the same thing as a directed expenditure, i.e. "earmark." That means that taxes the company/organization/group of people would have paid is not going in the federal budget - thus they get a special exemption while others do not.
I'm not saying its always a bad thing and in fact believe these incentives can be very productive -- but then you have to accept the fact that some directed expenditures (the other so-called "earmark") can be equally productive.
But just like some "bad" earmarks (which depends on where you sit) many of the tax credit earmarks are simple give-a-ways to those who don't deserve it while the rest of us pay.
So, in the end, CNN was right. They don't pay their taxes with costs X amount of tax dollars not in the budget, thus a bigger part of the burden falls on the rest of us. (And spare me the macro argument about whether anyone should ever pay taxes).