The 50mm f/2.5 Compact Macro lens is not a "true" macro lens. It does not magnify 1:1 (i.e., 1:1 means that the size of the image on the sensor is the same as the actual size of the object); it only magnifies 1:2.5. So, it doesn't let you get as close as a true macro lens like the EF 100mm f/2.8L IS USM Macro.

In addition, the design's a lot older. It was introduced in 1987, while the 100L Macro is a much newer digital-era design from 2009. The 100L is also an L lens (Canon's "luxury" line of pro lenses which are typically considered their best (but most expensive) offerings), with a UD (ultra-low dispersion) element, and its "Hybrid" IS unit is also relatively special in that it can correct for two types of shake (shift and angular), rather than just one (angular), like most of Canon's IS lenses do. Whether it's "worth" the additional cost is up to you, and how much handholding you plan on doing.

"True" macro Canon alternatives you could consider would be the older non-L EF 100mm f/2.8 USM Macro (note there's no IS), or the EF-S 60mm f/2.8 USM Macro lens (which can only be used on crop). These both cost more than the 50mm compact macro, but far less than the 100L Macro lens. Depending on what you plan to shoot, the longer lenses may be more useful by allowing you to use a larger working distance and not scare off critters that can hop/fly/crawl away when they sense you looming right over them; although, of course, with wildlife of any kind, field craft will be more important than the length of your glass. Shorter lenses and small working distances, however, are less of an issue with flower or product shooting.

I once shot a pretty bug with a midnight blue body and bright orange wings with my EF-S 60mm f/2.8 USM Macro on an XT/350D. It was only later that I realized I'd shot a tarantula hawk--a very large hornet with a very painful sting--from a distance of roughly six inches. If I do it again, it'll be with my EF 400mm f/5.6L USM on extension tubes. Maybe. If I don't run screaming first. :D