Mosques being taxed? Forget about it! They're given subsidies from temple money! Even the Muslim charity system (the Waqf boards) receives temple money.
I'd say that the state should stay away from religion. When people give money to a temple, they are effectively giving it to their co-religionists. If they wanted to give it to everyone, they could have given it to a secular charity. By destroying this exclusivity ("Only people of MY religion have a right to the money I give them"), you destroy the very purpose of a separation of religion and state in the first place. The religious sphere must he separate from the state, which is secular. By taxing religious places, you effectively place them in the secular sphere, which is a clear violation of the separation principle.
It is also a discrimination against religions whose people are richer, or whose religion demands that they give to charity through their respective religious institutions.
As an interesting titbit: Earlier, the Vatican was the largest concentration of religious wealth in the world. Now, it is the Tirumala Tirupati Devasthan (a major Hindu temple).