It’s been 3 days since I got my 2006 Lexus ES330 back from a body shop (I got rear ended!). I don’t know if I was imagining it, but when I was driving it today, I thought the noise level was high. The engine was quiet, so it must be some kind of road noise. I was driving on the same route that I had used hundreds times before. The tires are about 1 year old and seem fine.
If I’m correct to assume that body work resulted in more noise, what could cause it?
Yes it can. You’d be surprised how small of a protrusion can cause a noticeable increase in wind noise. Even a windshield installed half a millimeter too high on one side can do it. As for other noise, yes, if the materials are cheap, wrong, or installed improperly then more vibrations can transfer through the body to the cabin, resulting in more road noise.
As to what specifically could be causing yours, that’s pretty much impossible to tell you over the internet. Even in person it can be hard to track down noises, because they generally only happen when the car is moving, and it’s awfully hard to get someone to agree to ride on the bumper so they can listen for the problem 
So, what can be done. Should I get a second opinion about the body job? Should I take the car to a dealership?