They want to make the chapel less “faith-specific:”

“In order to make the Wren Chapel less of a faith-specific space, and to make it more welcoming to students, faculty, staff and visitors of all faiths, the cross has been removed from the altar area,” Engimann said.
The cross will be returned to the altar for those who wish to use it for events, services or private prayer. Student tour guides have been directed to pass any questions or complaints about the change on to administrators.
The cross was in place because of the College’s former association with the Anglican Church. Though the College is now nondenominational and became publicly supported in 1906, the room will still be considered a chapel.

This is why people are becoming less tolerant of religion, it’s being driven out of the public eye, into a private space where only those who find it tolerable are able to view it. This makes us quicker to say, “Remove it, it offends me.”
If they intended to use the space for something else, maybe they might want to stop calling it a chapel since that word has a specific meaning. According to The Free Dictionary, the word “chapel” is defined as:

a. A place of worship that is smaller than and subordinate to a church.
b. A place of worship in an institution, such as a prison, college, or hospital.
c. A recess or room in a church set apart for special or small services.
d. A place of worship for those not belonging to an established church.

After all they are a college and should set the example of using words properly.
(Link via Michelle Malkin)