I found it worthwhile querying small presses directly; had several nice interactions with acquisition editors and so on, and got a fuller picture of trade publishing than I would have otherwise, but you will want to look through the presses one by one to make sure they are legitimate.
Many start out with a specific goal (I targeted presses with an ecological or social justice mission.) Others feel more like an attempt by a group of authors to boost their work by forming a 'publisher' label. (Our writers club, for instance, has joked about doing this--I hope they don't and doubt we truly would. But it's easy to see how some similar clubs elsewhere might choose to try it.)
Piece of advice--Start lurking through the Bewares, Recommendations and Background Checks forum. Search on the press you have in mind. You'll see tons of small presses and get a good sense of them quickly. Many threads are dedicated to a single press. Makes it easy to check on people's experiences.
In the end, getting onto the bookshelves of bricks and mortars might be one of several goals that you develop. Finding the right press, and a good acquisitions editor with whom to work, might be another.
(FWIW, the CNR rate with small presses was similar to the CNR rate on agent queries, in my experience, including for presses that promise a response within three months--see e.g. Parvus Press in BRB forum).
(ETA: Oh and a couple independent bookstores said they'd put my self-published book on their shelves. A place in Denver, and a place in Lansing. Sometimes, local independent bookstores will stock your book too, if you ask. For this to work, if you want your book on the shelves, it needs to be available for them to order outside of Amazon, like from Ingram Spark, for example.)