When he took over as the shogun, Tokugawa Ieyasu had a very large family. He used this family to directly control around 1/4th of all land in Japan, as he could replace anyone he thought could be a threat to him with one of his sons.
Along with the loyalty pledge he made the daimyos sign, sankin kotai also worked to keep the daimyos under his watch and prevented them from rebelling. Sankin kotai, or alternate attendance, required each daimyo to live in Edo every other year. They could go home after that year, but the next year their wife and heir had to stay in Edo. Some daimyo stayed in Edo full time.
Ieyasu guaranteed that if the daimyo would be loyal to him, they would have unchallenged power over their land. After a hundred years of fighting, the daimyos liked this.
As the daimyos would be away from their land for a year at a time, it would have been hard for them to plan a rebellion and actually go through with it. Also, since they were all in Edo, they were all being watched by the shogun and his people. Staying in Edo every other year also made the daimyos closer and more friendly to the shogun, further lessening the chance of rebellion.
If the shogun learned of someone's plans to rebel, he would send his army to where the daimyo's wife and heir were living and kill them both.
This system also financially burdened the daimyos, the shogun required the daimyos to have a nice castle in Edo. Daimyos would begin to spend a lot of money to make sure their castle was the nicest castle, leaving many of them with little money (Gates, "Samurai").