Saving file as .m causes it to save as comments

Only initialization cells will be saved as uncommented code.

Check Cell -> Cell Properties -> Initialization Cell and Initialization Group.

You can also use Code cells (instead of Input), which have the Initialization Cell property by default. Alt-8 or Command-8 inserts a code cell.

You can check that it is an initialization cell by looking at the top right corner of the cell which has an extra cross:

Anything which is not an initialization cell will be commented out.