Going back to the 79th Congress in 1945, Democrats have controlled the Senate 24 times, Republicans 14. Republicans have held it for the last 3, Democrats for the three before that.
They used to teach civics in the 8th grade. The system was set up for the House to provide proportional representation, the Senate to provide State representation. The basis for this article seems to be a complaint that the Senate isn't providing proportional representation. It's not supposed to.
It's working exactly as designed. Matthew Yglesias should have taken a civics class.