On the documentation:
http://docs.opencv.org/2.4/modules/core/doc/basic_structures.html#mat
It says:
(...) if you know the matrix element type, e.g. it is float, then you can use at<>() method
That is, you can use:
Mat M(100, 100, CV_64F);
cout << M.at<double>(0,0);
Maybe it is easier to use the Mat_ class. It is a template wrapper for Mat. Mat_ has the operator() overloaded in order to access the elements.