If you go down to "Thread Display Options" in "Edit Options" in your User CP, you will see that there are three ways to view threads: "Linear," "Threaded," and "Hybrid." Linear is the default for most, it simply displays posts to a thread chronilogically, be it oldest to newest (most typical) or newest to oldest. Threaded organizes threads so that posts are grouped based on responses to other posts in that thread. For example, if you were to hit the quote button on a post, and reply to it, and you set your preferences to threaded display mode, instead of your post showing up at the bottom, it'd show up threaded below the post you just quoted (a little confusing I know). Hybrid is simply a cross between Linear and Threaded.
Moral of the story, the quick reply box is disabled until you click a post to reply to for the benefit of those who use the threaded mode so that posts stay organized instead of just becoming a mishmash.
ETA: At the top of the first post of each thread is a "Display Modes" drop down box where you can easily toggle between the various modes.