Religion and State and the IRS

According to a recent article in Politico, the IRS appears to be investigating whether Jewish religious groups entitled to 501(c)3 tax exempt status have compromised their status by their "political" support for the State of Israel.  According to Politico, and unnamed Jewish organization received correspondence from the IRS asking "Does your organization support the existence of the land of Israel?" and "Describe your organization's religious belief system toward the land of Israel.""

Of all the religions protected by the Establishment Clause in the Constitution, Judaism is unique in that Jews actually have their own country.  Technically, the Catholics also have the Vatican, but there are very few if any geo-political issues compromising the Catholic Church in America and its relationship to the Vatican as an official state.  It seems a little bit unrealistic if not downright unfair to question the tax exempt status of a Jewish organization simply because they support the Jewish State and its right to exist.  On the other hand, if we are not going to extend tax exempt status to political organizations, which we don't; then how do we separate religion and state regarding tax policy?  This has also come up as an issue when conservative evangelical pastors and/or their churches have made endorsements for political candidates.  It appears that this is not an issue that is going to go away anytime soon.