Obstruction is a personal point of emphasis for me and a part of the game I don't think is called as much as it should be.
For a long time, obstruction was a coached tactic by the defense since most umpires weren't calling it if the runner wasn't knocked down. I think that situation has improved a bit over the last few years as obstruction has become more of a focus and more umpires are calling it when it happens.
I agree that upwards of 90% of obstruction calls do not result in any further action by the umpire...call it anyway. I have had a few savvy coaches pick up on the call and coach their runners appropriately. I've also had a few that pick it up and think that their runner now has free rein to keep going as far as they want......
Bottom line...call it every time it happens.