Depends on the situation at hand.
For arguements sake, if you are playing a long iron into the green on a par 5, depending on how deep the rough is - it could turn the head over the end result being that the ball could still end up in the rough 5ft further away from you.
So instead of being 250 yards away from the green for 1, you are now 245 yards away for 2 and still in trouble.
If you could have got a 8,9,pw at the ball and moved it 70ft down the fairway or more, you are now 180 yards out for 2 with a much more makeable shot to hit the green for 3.
Its a hard thing to do, to choose to play a lofted club and knock it down the fairway a little rather than going for glory. Its all about the percentages, and giving yourself the chance to make putts - you cant do this from the rough.
If the ball is sitting nice in the rough, or the rough isnt too deep then you can risk getting a longer iron at the ball.
Ask yourself the question, would you rather lose 1 shot or 2/3 shots because of a loose drive?
Its not set in stone, there are times when you can risk the long iron shots, but this is part of your own game you need to learn.