I'm curious, what was the issue with Hipmunk? I've used it a few times for flights, and that's worked out well. No so good for hotel search? Punished mercilessly sounds pretty bad. I know that they use orbitz for flights, do they use another service for their hotel search?
http://www.tripadvisor.com/ShowUserReviews-g60971-d73363-r11... Compare and contrast: http://www.yelp.com/biz/howard-johnson-flagstaff
http://www.yelp.com/biz/howard-johnson-inn-flagstaff
(same place) Hipmunk lists this shithole as the #3 choice in Flagstaff. Having stayed there, I would say this is right on: "The lady at the desk, who seemed very nice, told me they only had double rooms, but that she would charge me for a single if I agreed to only 'dirty' one of the beds. Bad sign. So I show up in the room. At 3 am I finally go to get under the covers. I lift the top sheet off the bed, and I kid you not, someone had TAKEN A DUMP right there on the bed." They hit me for a $10 "key deposit" (cash only - they took the 4 grubby bills I had) to give me a key that didn't work, then ran my card for $85 instead of $52 ("the number is right above it on the keypad!") and tripped the fraud protection on my credit card. On the plus side, they were right across from an auto parts store and (supposedly) a pretty good pizza place (that was closed for renovations). On the minus side, they were right on a busy freeway, across from which was a major BNSF railroad spur, and shared a parking lot with a nightclub that played Mexican polkas until 2am. So. Yelp: 4 1 star reviews. Hipmunk: #3 in the city by "ecstasy."
EDIT: No wait, my bad that's a different Ho-Jo, it seems. Looks like there's two. Sure you didn't book the wrong Ho-Jo? The route 66 ones seems pretty far down in ecstasy. :)