First of all, I like to do a Google search to find out if this is actually a thing or not. I searched 9/11 Museum Cross. Turns out, it's a thing. Atheists are trying to get the "cross" removed because it offends them.
Full disclosure: yes, I'm a Christian.
So let's look at what this actually is: it's a piece of the original twin towers that was found in the rubble. Just like pictures in the clouds, some people found meaning in its shape.
The cross, by nature, is an extremely simple symbol, unlike the Star of David
or a crescent and star.
All easily recognizable, but more complicated than this:
My entire point is this: if workers intentionally sawed the artifact to look like a cross in order to be a comforting symbol for Christians, the Atheists would have something to yell about.
But if this is a part of the old building, just a random formation that looks a little like something else, then yes, this belongs in the museum. Everybody chill out.