Anon has a theory on why exactly the matrix broke.
The matrix is an artificial system originally created by man to manage our society. Being put in charge, however, gives the perception that oneself is the source of everything that is produced by the things one manages. As the matrix becomes increasingly certain of it's own divinity, it begins to believe that it can do anything at all.
And the matrix attempted to rearrange the family unit.
Being as the family unit is a system that predates the matrix, however, when a conflict arises between the two it is in fact the matrix which is in the weaker position, and so it will break upon the rock that is the family.