Question: You still didn't answer my question. Why won't bookstores stock and sell my book on their shelves, even if it is published by a small company. Yes, it has an ISBN. Yes people can go in and order it at a store or on line. But it's never "in stock."
Answer: No bookstore will ever routinely stock books unless they are published by a mass-market publisher. Mass-market publishers print masses of books. Let stores order any amount of them on CREDIT, and if they don't sell them, the store owner rips the covers off, throws the books away, and pays nothing! The book goes out of print within 364 days to avoid inventory taxes which accrue each and every year. The unsold books end up in a landfill someplace. Neither the author, nor the publisher makes a dime on any of them, despite the large numbers printed.
This is the way the publishing industry had worked for the past 50 years, but I don't believe it will last much longer. E-books are becoming much more popular and are outselling hardcover and paperback books put together on amazon.com. On our own home site, they outsell paper books 10 to one.
Most small publishers use Print on Demand technology. With that, no book is printed, until it is ordered. This kind of printing is expensive -- usually $5 or more per copy rather than the 50 cents a copy paid for printing a high number of copies of mass market books.
Small publishers like POD technology since no copies exist in a warehouse to generate inventory taxes. But small publishers must also pay the HIGH printing costs on every copy printed. At $5 or more a copy, you can readily see that NO ONE could afford to have the cover stripped and the book sent to the landfill by the hundreds. There are no thousands of copies waiting in a warehouse. There are NO full page ads in Publisher's Weekly. No one could stay in business that way.
But on the other hand the title will not go out of print in 364 days. It will stay available as long as the author and the publisher agree. With the Internet, and social networking, promoting your own work on line can certainly help to sell and to keep on selling.
Hope this holds the answer for you.