I have often done as you suggested.....draw around the ruler with a pencil, then cut out the motif. But you don't necessarily have to use scissors. With a drawn line, I sometimes use my favorite ruler to get the straight edge for my rotary cutter. Then I lift & reposition the ruler for the next side. It's a little bit more work, but I think it saves time over using scissors. Of course, sometimes using scissors is better.
Also, to mark the motif being fussy cut, sometimes I make a template from a piece of manila folder, cutting out the center in the size and shape I want (including seam allowances of course). Then I position the opening over my design and draw my lines. The folder paper is heavy enough to use over and over. And when I've finished marking all the designs, I slip the template into the pattern package to save for another time I want to make the same quilt with fussy cut pieces.