Those are all good questions. They're also difficult questions, but important for Christians to discuss.
I don't take issue with the concept of Christian bookstores, even inside local churches. If a pastor finds a book that has helped him in his walk with Christ, he may recommend it to the congregation. Stocking that book in the bookstore makes the book immediately and conveniently available to the congregation.
The bookstore can also stock resources for Sunday school classes and small Bible study groups.
As for other merchandise: Other items, such as key chains and bumper stickers, may help Christians memorize Bible verses or help them drive more politely than they would without the bumper sticker identifying them as Christians. Others see those items as tacky merchandise.
It comes down to the motive behind the product, which we can not determine with 100% certainty. We, as Christians, should always be on the lookout for other people--Christian or not--looking to exploit us for their personal gain.
I believe businesspeople using churches for business networking or, even worse,
MLM (multi-level marketing) recruiting is cause for greater concern than Christian bookstores. The practice of MLM recruiting is rampant in some churches (at least, it was in Oklahoma).
If you hear someone at your local church touting the benefits of selling Amway products,
run. Jesus may have driven the merchants out of the temple, but
you're not Jesus.
In all seriousness, if you see someone exploiting other church members, explain your grievance to the person privately or report the situation to a person in authority (e.g. elder, bishop, pastor, reverend, priest).