Again, there are those who might be better able to explain it than I am, but here is what I've gathered from previous conversations:

With different subspecies, there are enough distinctions between genetic traits to differentiate them as different animals. These distinct traits enable the different animals to survive in their native environs. However, if you cross-breed different subspecies, the resulting specimens will not have those differing traits as strongly prevalent, which, under the right circumstances, might make them less capable of surviving. It might also introduce new traits that might bring long-term harm to a breeding population.

And keep in mind, we're not talking about animals of a single type, like dogs (all of which belong to canus lupus familiaris), but of different types, with enough genetic distinction that they are not classified the same.