1. Get and read The UNIX Programming Environment by Kernighan and Pike.
https://www.google.co.in/search?q=the+unix+programming+envir...
A classic. Outdated [1] some, for modern Linuxes and BSDs, so:
2. Supplement it by reading Linux / BSD man pages and get a book or two on one of those OSes, or other Unix variant you are using, such as Mac OS X.
[1] But you are unlikely to find another book that better conveys the Zen of UNIX, so to speak. The authors were early UNIX users and developers, and Rob Pike (now at Google) is one of the creators of the Go language.
Well, that is to be expected given the fragmentation in the UNIX world.
One never knows how the specific UNIX is going to behave, which command line arguments are available besides the common ones and what sort of POSIX undefined behavior exist.
You will evolve your own style of command line usage from what you read and what you are able to remember. Even very skilled people will do things differently.
If you want a classic though, check out Unix Power Tools at O'Reilly
EDIT: changed ascii asterisk in front of all instances of nix to u+2217, the plain asterisk translates to large bodies of italicized text on HN. Which I knew.
Yes, that's very good. If I was to compare it with my recommendation in this thread, of The UNIX Programming Environment (UPE), I'd say that the Power Tools book is like a cookbook, while the UPE book is like a tutorial (but a power tutorial :)