From an article of the same title (subtitled "Even Unbuilt, Jerusalem Tolerance Museum at Center of Fight Between Jews and Muslims") by Matti Friedman on abcnews.com:

The Museum of Tolerance started off with good intentions, over $100 million in donations, an eye-catching design by architect Frank Gehry, a 2004 kickoff ceremony attended by Arnold Schwarzenegger, and a great piece of Jerusalem real estate.

But underneath that real estate, it turned out, there were Muslim graves. As a result, instead of bringing this contentious city's warring tribes together, the museum has sparked a fight with political, religious and historical dimensions between Muslims and Jews and all this before it has even been built.

Months of arbitration have ended in deadlock, the site is enclosed in aluminum walls, and the dispute is now before Israel's Supreme Court. Even if the court gives the go-ahead, however, the Museum of Tolerance could well remain permanently tainted by allegations of intolerance.