Indeed. I'd be interested in seeing if someone could mentally dissociate themselves from the Peter Jackson movies (as well as the previous animated movies), to not wind up being strongly influenced by them. It'd be tough. In my mind now, Peter Jackson's Middle Earth is Middle Earth.
There are parts that are amazing. All the key locations look right. Shire is amazing, as is Rivendell and the Misty Mountains and Moria. Erebor and Dale both looked great from what we saw of them.
Rohan was all wrong though. Too rocky. Minas Tirith looked fantastic, but the Pelennor Fields were horrible. It's described as lush green and full of little farms. Not a barren field. And where is the Rammas Echor. You know, the actual thing that gave the Pelennor fields its name?
Mordor looked great when you only got glimpses of it from the outside. But it didn't seem too bad once Frodo and Sam actually got there. It should have been darker and less accommodating. They should have included scenes where they were drinking water that tasted like oil.
Similarly, Dol Guldur seemed off to me. I never imagined it being so..ruiny. The book seemed to imply it was a sort of second headquarters for Sauron. A strong fortress that required the combined strength of the greatest people alive in order to penetrate. Not the sort of place a lone wizard could walk willy-nilly into without being accosted by Orcs or trolls or cruel men. Mirkwood also seemed too bright, but I guess that's because they decided to portray it as still Greenwood. Hopefully by time the Dwarves get there, it will be the black German-fairy tale forest full of mutant animals and enchanted streams I imagined it to be.
Finally, the area around Rivendell is all screwed up for me now because of that dumb Warg chase scene. It's pretty clearly depicted as some pretty dense forest. Apparently the Trollshaws are tiny and most of the land now is empty field that looks suspiciously like Rohan.