For the same reason why many of the dinosaurs were killed off in the last major Ice Age, anonymous. Although modern-day dragons have adapted to withstand colder climates, they are still not fully adapted to withstand abrupt drops in temperature. Many dragons do not possess an insulating layer of fat, fur, or armor the way many other species of pokémon do, so they’re far more susceptible to things like hypothermia. It doesn’t help that many of the more famous dragon-types are also partially flying-types, which itself has a weakness to ice due to the fragility of their wings. (Freeze a flying-type’s wings, and you effectively disable them.) Seeing as the wings are of an additional importance to dragons due to their integral role in thermal regulation, this makes dragon/flying-types such as dragonite even more susceptible to lower temperatures.
In other words, dragons are weak to ice because they’re not well-adapted to colder temperatures. They are, however, well-adapted to succumbing to hypothermia.
The Pokédex According to Bill 