The Fodor article on travel booking sites..
 

I think anyone can recognize their selling tactics; " only two rooms left!"
" 27 people are looking to book this RIGHT NOW!"..and other variations of pressure tactics. Typical in
all sales situations...but that doesn't make it acceptable for them to use such ploys. I find reading posts
in forums from travelers who have JUST posted reviews of their stays right after staying there helps, but
even then, I assume there are ringers for those chains who benefit($$) from positive posts. On the other hand
I'm sure there are those who post negative reviews( ..source being competing chains/hotels..) for the same reason.
And then, there are some who just like to post pissy reviews because NOTHING makes them happy, because
they're basically miserable in general. Careful scrutiny of reviews can lead you to the right hotels.
I disregard the best and worst reviews therefore, then examine the ones in between carefully, taking all reviews into
consideration to find which are probably the honest reviews. I might also recommend the Oyster site. Just look it up, it's good.
Overall, just do your homework and you'll usually be happy with your choice. AND..AND..before I fail to mention it, ALWAYS
check directly with hotels online or by phone for their rates. They'd much rather you book them directly. Booking directly
avoids so many issues, should you need to cancel, and you'll get the straight scoop from them on their hotel.

You are correct that you should check directly with hotels when possible. Some hotels, like cruise ship companies, however, will not match some online prices, even though they can save commissions. They feel that diminishes their brand. Some discounters like Hotwire offer unnamed hotels for less (although their add-on fees will bring you closer to the otherwise lowest price on a particular hotel). We have noticed, if you are worried about getting an unwelcome surprise, that it sometimes is obvious which hotel you will get. The small print often says the last person got such and such hotel, and our experience is that is the one you will get. Additionally, they tell you the number of trip advisor reviews for the unnamed hotel, and you can usually look at the named hotels and figure it out. We just did that for a couple of Copenhagen bookings and did save a few dollars. Hotels and cruise ships do have slow times, do need to discount during those times, and they have to figure out ways to do it without offending those who have paid or will pay the higher prices.