Most definitely not. Now I have not seen/read Shogun so I don't know how it's depicted, but villages definitely wouldn't just accept their fate. In fact, if anything the villagers more often than not stood up for themselves, and being too harsh on the villagers could lead them to (illegally) escape the domain or even rise up in revolt. If this happened it would reflect very badly on the responsible samurai, and bring down the ire of the domain or even the Edo Bakufu, not to mention it would decrease the clan's revenue and a revolt would at the very least heavily increase the clan's expenses to crush it. Case in point that the Shimabara rebellion was caused predominantly by over-taxation, and the offending clan was destroy by the Edo Bakufu itself. For the most part villagers were ran by village elders, and the clan/Bakufu rule was fairly reasonable and fairly off-handed. A lot of times in the Edo people would riot over taxation or other issues, and while the ringleaders were usually punished the government more often than not gave in or compromised with the people. Even the most famous privilege of the samurai, that they had the right to kill any commoner that insulted their honour, had specific rules that if not followed would be ruled as murder and so rarely happened.

That's not to say that the samurai had the commoner's best interests at heart. Just a few decades ago marauding armies regularly burnt villages. See here for more details.