They weren't exactly civilan populations though were they? Hitler declared "total war" - effectively everyone was part of his war machine
Bombing the cities disrupted the military supply and distribution chain. A very legitimate target
2/3rd's of Germany voted AGAINST Hitler - these people were just unfortunate to be caught between madmen. As for attacking legitimate targets, bear in mind that Churchill himself referred to it as 'terror bombing'. Most of the civilians that the British and Americans dropped incendiaries and white phosphorus (now banned under the Geneva convention) on were woman, children and those too old to fight. The majority wanted nothing to do with Hitler.
Then there are the nukes. Not nearly as bad as the terror bombing campaign, but still an extremely cruel thing to do.
It saddens me that i should need to explain why there are no good excuses for attacking civilians, ever. Do we really suck that bad as a species?