Recently I was having problems with WordPress overwriting my .htaccess. I wanted to do some URL rewriting, but WordPress kept erasing my changes. I realized that WordPress reserves a portion of the .htaccess file for itself, and it is clearly marked as such. As long as you don’t put your edits in that spot, they won’t be overwritten.
If only I’d read this article first, I wouldn’t have been scratching my head over this issue