It's puzzling to me that a group of people that deal with commerce would not almost immediately become the most powerful class excluding royalty and the shogunate. I know that eventually merchants became powerful in Japanese society, especially during the 19th century. But what kept them down for so long? In many societies, 'merchants' are often at top of the social strata, and it's hard not to imagine them being at or near the top universally.
That is a common misconception about how Japanese society worked in the Edo, from the emphasis of Edo's use of Neo-Confucianism and the idea of the four groups society. Merchants were considered lower than the other three only philosophically, and often not even then. You can see here for more details.