I've found it easy to avoid misusing Ctrl-w because of the fact I use it so much to close tabs in Firefox. You just need to have two different uses for something, both of which you use very regularly, to get used to not accidentally misusing them, I've found.
Alas, I think you may be right. I haven't been using it very long.
Once I actually buckled down and started learning how to use it, I was surprised by how quickly and easily a natural feeling of "this is how it should be" developed while using Vimperator. Of course, there's a lot of positive transference of knowledge from my heavy use of Vim itself, but still -- I didn't expect to find it this easy.
I think part of the reason may be that every single keyboard-driven browser I have ever used before (Lynx, W3m, Links, et cetera, ad infinitum) was so awful as a Web interface that I became convinced Web browsers were a uniquely GUI-suited type of application. Vimperator is definitely changing my mind.
