I don't have a beta, or use Ctrl+F, or submit to ff.net, but I still keep my chapters as separate documents. It's easier for me to post my chapters wherever I do submit them (like on LiveJournal) because I just hit Ctrl+A, Ctrl+C, Ctrl+V, and there's my chapter in three steps.
See, my chapters (depending on the fandom) are long. Like, for one of my Digimon fics, a chapter is around thirty pages typed. It's easier for me to find a particular scene in thirty pages than it is to find a particular scene in eight-four pages (which is how long said fic is when put all together).
I also just like the way my fic's folder looks when I open it up in Windows Explorer, and see each chapter's document. I like the organized look.
Plus, if I want to write a chapter that's farther ahead in the story than what I already have written, then it's just easier for me to have it in a new document instead of trying to figure out where it will fit in one huge document.
Also, if I need to check something that happened in a previous chapter, I don't have to scroll all the way back up. I just open up the old document, which opens automatically in a new window, and can flip back and forth easily to make sure things match up.
That's why I do things my way. Just easier for me.