There is no question the USAU rankings are messed up. Just look at UCSB as one example. They played in the finals at the Santa Barbara Invite, losing to Stanford. Then they won Stanford Invite, avenging their only loss. And they're #9?! Please.
That doesn't mean that the rankings aren't doing their job. They aren't designed to pick a champion, but rather to assign wild cards. The if-it-ended-today list is California with 4 bids, the PNW and the Cold-and-Snow with 3 each, the AC, Great Lakes and Cowboy divisions with 2 apiece and everyone else with one. You can quibble with whether or not one bid is a good idea or not (it probably isn't) but that's the system we've got. Looking at the list and knowing the teams on the bubble in each region (Western, Sonoma, Wake, Penn, Iowa State...) I don't think the allocations are unfair. It'll be interesting to see how things shake out after Easterns and Centex.