While larger animals would be more preferable due to having more meat, there are trade-offs in how easy an animal is to handle. The larger the animal, the more serious the consequences if that animal should intentionally or accidentally injure you. A smaller cow would also be much easier to physically handle, as in "leading the bull by the horns", than a larger animal. There may also be a relationships between aggression and size, perhaps a hormonal one, and so selecting for less aggressive animals might have an effect on size as well.

I hesitate to cite Jared Diamond, but this article is a pretty good overview of the physical changes that occurred during domestication and how the traits that made a species a good domesticate relate to these changes. Just ignore the nonsense in the second half of the article from "Why there were so few homelands of agriculture" and down.