The canon 60mm is superb- not just to start with, but to keep as a main goto lens thanks to its great optics and is responsiveness. I started with the canon EF100 mm f/2.8 USM and had difficulty with depth of field and blurry images. I opted to then try the 60mm and it was more user friendly for me. I later learned more about taking control of my camera settings and after practicing, switching to manual, reading books, taking clases with underwater professionals and practicing, I was ready to pick up the 100 mm macro back and it was a better experience for me the second time around.
They are very similar, but the 100 mm will give you advantages is certain situation where the 60 mm may be a bit wider, or may need for you to get much closer as compared to the 100mm lens. Well, you do want to get very close, but that's another topic....
They have a newer lens now, the EF100 mm f/2.8L IS USM and while I have not tested this version of the 100 mm canon with Image Stabilization, I understand they are pretty much discontinuing and retiring the EF 100mm withouth the IS, but optically speaking, they are very close to each other.