How do you motivate subordinates when you have personal doubts regarding a mission?

As long as the orders are legal, then your commander's decision is your decision. The sooner subordinate leaders realize that, the better off they'll be.

Have I had to stand up in front of my units and tell them they were about to be given a bad deal? Yes. Did I place blame? No. The situation was what it was. Our mission is to make the best of it and execute.

The problem we all run into, especially when we're younger, is we mistake being liked for being respected. Front line leaders (normally junior officers or NCOs although there are senior ones that do it to) throw leadership and decision makers under the bus so that they look like the bad guy. Although this may make you look good in the short run, it is prejudicial to good order and discipline and a cancer to the unit.

I like this question, since it's so common to deal with. Actually, the first response that came to my mind was something you SHOULDN'T do in this situation. If you want to keep your guys motivated, you should never say, "This mission sucks and it's some higher-up's dumb idea, so let's just do it." Doing this just creates resentment up and down the chain of command, when you and your guys may not have full visibility on the big picture. I suppose there are arguments against my point, but just my perspective.

You keep your mouth shut and lead.