Why are certain folders 'hidden'?

Can't figure this one out: some folders are, by default, hidden in Finder, particularly
Macintosh HD/users/me/Library
The only way I can make it visible is to use Onyx or a Terminal command, which also makes tons of other files visible, which I don't necessarily need. Why is the 'Library' folder hidden and how can I make it show in Finder without using funky commands to make it appear? Also, I'm assuming that there are other such folders, that I might not need right now, that are hidden...
I've rebuilt all the indexes I can find, but to no avail. Any ideas out there?

~/Library is (or should be) the only hidden folder in your home directory.  Apple deliberately chose to hide it in Lion to keep people out of it - the idea is that it's where applications store data, etc, etc that is specific to your account and that there's no reason for users to be mucking around in it themselves.
And given how many times people have shown up here with problems they've created themselves by mucking around in their Library (or /Library, or /System) I can't say that point of view is totally unwarranted...
However, actually getting to your ~/Library if you do need to is still relatively easy...open a Finder window.  From the menu bar select the "Go" menu.  All the same choices (generally) as are in your sidebar should be there.  Now press the "option" key.  Your Library should appear in the menu.  Click it and you are there.
Now, while ~/Library is the only hidden folder in your home directory, there are tons of hidden folders in the system root...and you would be well advised to stay out of them.  These include:
/etc (which is really /private/etc)
/tmp (which is really /private/tmp)
/var (which is really /private/var)
And others.  Plus some hidden files.  Unless you're feeling particularly Unix-y, you should really, really leave them alone.

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