Looking at this in terms of sets, let's call O the set of all owls, and F the set of all things that can fly. What this original statement is saying every animal that's a member of the set of all owls is also a member of the set of all things that can fly, or in other words, O⊂F (O is a subset of F). Negating this tells us that, while there's at least one element of O that also belongs to F, O is not contained entirely in F (O⊆F, in notation), so a good negation or our original statement might be:
Not all owls can fly.