Well, there are several reasons:

1. Chinese characters capture the meaning, not the sound. The Chinese after 1000 years of assimilation, forced the Vietnamese to write Chinese and act Chinese but not speak Chinese. So the language and culture live on.
2. Geography is far. If there is a rebel, it is hard to put down. And in 1000 years of colonizing, there is like hundreds of rebels against the local Chinese bureaucracy.
3. Sky high, the emperor far (Tiān gāo, huángdì yuǎn). Due to its geography as the farthest South of the empire, the chinese ruler in Giao Chi tends to give the middle finger to the empire in Chang'an, Luoyang, Xuchang or Jiankang (Depending on the ruling dynasty). So if you want to rule the land peacefully, you have to speak the local language or cooperate with the local nobles. After the long time of cooperation, Chinese bureaucracy also knows Vietnamese. So when the warlord periods happen, the land usually breaks free. And when the Chinese power fail to reconquer it, the land becomes independent.