"So, you're saying that even if they took the technology/concept from another environment (say mainframes or databases for the sake of discussion) then they still deserve a patent because they were the first to think of using it in a file system?"
If it's non-obvious, then yes - that's the law.
"Honestly, that concept to me is about at sane as Charles Manson."
Well, we haven't established YOUR sanity yet, now have we.
"The more I think about the actual concept it seems VERY similar if no the same as a basic concept taught in my high school's programming courses."
It may BE similar, that doesn't mean it's not patentable under current U.S. law.
"Besides, when was the technology first patented and then brought to market? 10-15 years?"
You're daft (you watch Faux News much? They use that same tactic).
NetApp filed for the earliest patent that Sun claims has "spurious claims" on May 31, '95. The WayBack Machine shows data from the NetApp web site talking about WAFL and stuff related to that patent in Dec, '97 (http://web.archive.org/web/19980201130313/http://www.netapp.com/technology/level3/3002.html#I36).