Open source DirSync Pro syncs folders on any platform
While it's got plenty of advanced settings that can be used to modify jobs, the default settings should work fine for most users. By default, DirSync will update any new or modified files (subfolder contents included) in your directories.
To change the sync direction, simply click on the two-arrow icon until it suits your needs. You can also set a number of backup sets to keep (up to 50) if you prefer a bit of redundancy, filter files to include or exclude, and perform post-sync deletions. Linux users can choose to copy symlinks as files or simply ignore them.
Creating and managing multiple jobs is an easy process - the only thing missing is the option to schedule jobs. I don't mind kickstarting synchronization tasks myself, so I don't find that to be a major downside.