Well, first, because the claim is made here constantly that Europe is a secular region, when it clearly isn't. You can argue about church attendance, but the statistics are funky in both places. Meanwhile, there are explicit connections between chuch and state in many countries, and open funding of churches by the state. From this side of the pond, where the government is both formally and in practice secular, European claims in that direction seem questionable at best.

Second, the potential conflict is that if Turkey is pressured to reduce her support for Islam, then she may fairly ask why France, Germany, Britain, Spain, et al. are allowed to support their churches. At that point, who gives in? Do the French cathedrals close due to having no members, and get turned into restaurants? (As happens in the U.S.) Does England allow the next king to be Catholic?

My view is that adding such a huge new member to the EU will cause big changes on both sides--and Europe is not officially admitting it. Europe may plan to press existing EU ideals onto Turkey, but an obvious reflex will be for Turkey to press her ideals on to Europe.

Specifically, how will European countries divide the financial support that they give to churches? Will it be by population, i.e. Muslim churches get, say 70% of the government money and Christian churches get, say, 30%--because there are so few Christians? Or will Christian churches get 90% of the money because Europeans are Christians after all?

Will the EU church-supporting fund have to be significantly enlarged to fix up all those Turkish mosques that desperately need repair? After all, with Turkey's huge population, and that population almost entirely Islamic, equity demands that EU cultural maintenance be distributed in proportion.
http://www.ndp.ie/viewdoc.asp?DocID=588