I'm so glad you asked.
The red square was crafted to be the symbol of student power- because as college students we are 'squarely in the red' (get it?). The sign specifically comes from student protests in Quebec, where students went on strike for lower tuition. (Read about it here) The Divest movement did not want to be lumped with the 'green' movement- we are new, mobilized and ready for action- and we know that climate justice is about more than the Sierra Club. So the orange square was chosen as a nod to student power.
Here's a great photo from another university divestment campaign (Image courtesy of http://breakingdowndivestment.wordpress.com/tag/fossil-fuels/page/2/)