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Ymir, seeing the power of the foreigners that accompanied his little brother and how they easily massacred his siblings, didn't even think twice about running away.
Ymir was strong, the strongest Blazing Ashura, and was born as a Divine Species, however, he valued his life over the others, and didn't saw any merit on risking it to save the people of his Nation.
Perhaps his father would have done it, but he, who never learned to value others, would never put anyone before him, and he would never decide to fight someone he couldn't win against.
Ymir left his mother on the castle, as he commanded all of his troops and civilians to form a massive army as the last stand, while he ran for his life, over the fastest fire lizard in the Nation.