Typically I take them off, but on the FX there are all kinds of vacuum lines, solenoids, misc wiring, plumbing, etc. It just looks messy and obiviously was laid out knowing that it would be covered. So I leave it on. In this case it is just a plastic ring with foam underneath, it still leaves the majority of the intake runners exposed, so at least it kind of looks like an engine.
A buddy of mine has an IS350 Lexus, his engine cover significantly quiets his fuel injectors - down to just loud.