I consider myself a small press, even though most of the books I publish are my own. Several of my titles sell well; in fact, one of them sells really well. My books have been in Deseret Book and Seagull stores, as well as in a lot of independents. I've had an LDS distributor for years, but I recently decided to self-distribute. Now Deseret Book won't even talk to me. They tell me I'm not big enough for them to bother with--even though they were ordering almost weekly from my distributor. I don't understand that. I'm starting to feel like the ugly step-sister.
This happens to a lot of smaller presses and self-publishers. As with so many other issues, a lot of it boils down to economics and the "economy of scale." There are certain overhead costs that are the same regardless of how many books are ordered--for example, the man-hours it takes to fax an order. Let's say you're ordering 100 titles. If a bookstore had to order all 100 titles straight from the author or publisher, that means 100 purchase orders, 100 faxes, 100 incoming invoices, 100 checks, etc. If they can order all 100 titles from the same distributor, that means 1 purchase order, 1 fax, 1 bill, 1 check.
Shipping costs are another example. The more you ship at one time, the less you pay per pound. So if a small bookstore orders 2 books from you, the cost to ship is about $1.25 per book. If they throw those 2 books on an order of 100 books, the cost per book to ship can be as low as 10-20¢ per book. Big difference in profit margin.
Many bookstores have a set of conditions that an author/publisher/distributor must meet, otherwise no matter how good the book might be, it isn't cost effective to deal directly with them. These conditions vary between stores, but a MINIMUM is usually 5-8 titles that "sell well." What "selling well" means varies from store to store too. Some bookstores will work with smaller companies, but will ask for special terms, such as a 50% discount or free shipping or both.
It's an uphill climb for the small publisher. I wish I had some better news or suggestions for you, but I don't. You could try expanding your product line, but that's going to increase the time you need to spend in your business which will take you away from future writing projects. And even if you have 40-50 books, you'll still have bookstores calling and asking "Why don't you go with a real distributor?"
Or you could do some concentrated marketing to boost the sales levels of your current books. If the public is going into the bookstores demanding the product, then the bookstores are usually going to work with you on some level. But advertising can be expensive and the most widespread is through the DB catalog (catch-22). Books 'n Things covers advertising through the independent stores. (I don't have contact info handy for them. Go into your local LDS independent bookstore and see if they have a Books 'n Things catalog you can look at.)
Last option, reconsider your decision to self-distribute.