May I direct you to the 1st Admendment which states:
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
So, it could be argued that by providing 'free' funding for this study, that the gov't is indeed establishing a religion; which is contrary to the 1st admendment. Secondly, if the State choses to fund religous schools, you are selectively discriminating against religions who do not require a degree in order to join the clergy; in that you are providing money to say ... Lutherns over Mormons (just an example - no disrespect to either party is intended).
It boils down to 'if you want to become a Mullah, do so on your own dime'. So, whether the religon is Luthern, Methodist, Buddist, Wiccan, Satanic (or any other); if that is your chosen pursuit, the taxpayer should not be expected to foot the bill.
Also, it has been brought up that society as a whole benefits from the educational support of engineers, medical professionals, teachers, ect. However, the only intended benefitiary of a Theology degree is the congregation to which the person belongs. Thus, as only a select group benefits, it would not be unheard of to expect that group to pay the costs.