There are a number of considerations to take into account; rather than try to list, there is a *much* better summary here:
(This summary discusses all of the 'connector' options for Tomcat.)
I have been using mod_jk due to the fact that it also works with the Tomcat 3.x releases (when I started using it, on Linux), vs mod_webapp which is/was advertised to work with Tomcat 4.x only.
Personally, I also find the configuration of mod_jk to be a bit more familiar, since a mod_jk configuration is nothing more than setting up a Virtual Host on the Apache side of things...
These considerations are good for simple sites, but you may need to consider much more if you are needing things like SSL support between Tomcat/Apache, etc.; I'll refer you to the summary above, with links, to find out more...