Not wrong per se, but as others have mentioned, you may well be stepping on some toes. If you don't feel like dealing with the owners of said toes (whether in the bookstore, or the relevant person in the university), then there are ways to do so without blatantly stating that the bookstore is ripping off students. (Note that I'm not implying that you are blatantly saying any such thing!)
One option is to tell the students on the first day of class. The obvious downside to that is that many students will already have purchased the needlessly expensive bookstore texts by then.
A better option is your practice of mass-email prior to the start of the course. Instead of urging the students to buy from Amazon (which may imnply that you are affiliated), why not just provide information on prices from the bookstore as well as the prices --for new and used-- from several vendors (Amazon is just a starting place, Abebooks, Ebay, Textbooks.com, etc, come to mind as well). Also, as others have mentioned in the comments, students will appreciate if you mention whether the latest edition is required, or if the previous (much cheaper!) edition will also work. The savvy student will know what you are implying for the alternate vendors, and the rest... well, perhaps they deserve to pay the bookstore prices!
Additionally, if your institution has a formal or informal student exchange, students may be able to buy used textbooks from a student who took the course last semester. You might be able to put your incoming students in touch with this network, as well.