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(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.