Same reason you can buy clothes at Macy's, JCPenney, Kohl's, Gap, Limited, Target, etc. Competition.
Amazon has their bookstore for the Kindle e-reader and Kindle app (Kindle e-reader was developed for Amazon)
Barnes and Noble has their bookstore for the Nook e-reader and Nook app (Nook e-reader was developed for Barnes & Noble)
Apple has their bookstore for their iBooks app (for iPad, iPhone, iPod Touch)
Sony has their bookstore for their e-reader
If you only want one source for books pick one and go with it. Your selection choice may vary or be limited though. Some books may be available across all platforms, but Amazon has been in the e-book business a lot longer than Apple, so of course their selection may be larger.
The Kindle and Nook apps are free for the iPad so I don't see a problem with downloading those apps and having the possibility of shopping their associated stores. sure the apps may have a few minor differences in features, but as long as it allows me to read the text I'm OK with it. On my iPad and iPhone I have iBooks, Kindle and Nook (Barnes & Noble reader on iPhone). If one does not have a book I really want to read, I will go to one of the others and can find it at one of the three choices.
Amazon and Barnes & Noble created iOS versions of their readers to open their marketplace to a larger audience. They understand that many who own an iPad may not want to buy an e-reader, or maybe after using say the Kindle app, may decide to buy a Kindle for themselves or as a gift for a loved one that may not necessarily want or need an iPad.