As Patently Apple notes, it's currently unclear as to why RIM is opposing the WebKit trademark.
Research in Motion has been granted until November 22, 2011 to produce their official opposition details. Until the contents of RIM's opposition are officially made public, we're a little in the dark. With that said, it wouldn't surprise me in the least if details of their complaint and opposition to Apple's WebKit trademark application eventually leak out by parties interested in seeing Apple's trademark application go down in flames. Time will tell.