That becomes more of a preference/design decision. Personally I like it affecting DoT's. Makes things like haunt more mitigatable. It also helps when the DoT portion is a different attack type than the application hit. I may be weak against the DoT and want to reduce that instead. For example, as a mechanical, I would be more worried about the DoT portion of Poison Fang
which is elemental damage than I am the application which is Beast damage. Not that a mechanical has Rake, but as a quick example.