Why the unix bin directory named in that way

Linux distributions use the FHS: http://www.pathname.com/fhs/pub/fhs-2.3.html

You can also try man hier.

I'll try to sum up answers your questions off the top of my head, but I strongly suggest that you read through the FHS:

• /bin is for non-superuser system binaries
• /sbin is for superuser (root) system binaries
• /usr/bin & /usr/sbin are for non-critical shared non-superuser or superuser binaries, respectively
• /mnt is for temporarily mounting a partition
• /media is for mounting many removable media at once
• /dev contains your system device files; it's a long story :)
• The /usr folder, and its subfolders, can be shared with other systems, so that they will have access to the same programs/files installed in one place. Since /usr is typically on a separate filesystem, it doesn't contain binaries that are necessary to bring the system online.
• /root is separate because it may be necessary to bring the system online without mounting other directories which may be on separate partitions/hard drives/servers
• Yes, /etc stands for "et cetera". Configuration files for the local system are stored there.
• /opt is a place where you can install programs that you download/compile. That way you can keep them separate from the rest of the system, with all of the files in one place.
• /proc contains information about the kernel and running processes
• /var contains variable size files like logs, mail, webpages, etc.

To access a system, you generally don't need /var, /opt, /usr, /home; some of potentially largest directories on a system.

One of my favorites, which some people don't use, is /srv. It's for data that is being hosted via services like http/ftp/samba. I've see /var used for this a lot, which isn't really its purpose.

No, they didn't. Some don't even apply to Unix. When Unix was in its infancy, there were dozens of operating systems out there, and dozens more came after its release. Many of them were on the ARPANet and many of them made it to the Internet. Some RFCs describe global things like the right way to write IPv6 addresses (RFC 4291), how MD5 should be implemented (RFC 1321), or why not to admire pigs flying overhead (RFC 1925). Others are more OS-specific, like Windows Kerberos password change protocols (RFC 3244).

A lot of what you see now are empirical decisions that later became standardised.

If you want to learn about Unix networking, your best bet is probably one of the books about Unix. If you want to learn about why things are the way they are, reading the source code of early Unices is an interesting exercise. But not an easy one. :)