If we are talking about the 3rd and 1 play I agree they should have run the ball with one timeout left. They weren't on the NE 20, which makes all the difference in the world. There were 22 seconds left and they were on the 14 yard line.
You have to pick up the first down on this play. And that would have given them a decent chance to pick it up. They pick it up and call timeout, which means they are now at the 12 yard line for all practical purposes, if not closer, with probably 12-15 seconds left. They don't pick it up they call time out and kick the field goal.
They make it and they now have three throws into the end zone. There aren't any more first downs to obtain to worry about not having a time out. You intstruct Flacco to throw the ball away if the play isn't there. You're fighting for three more plays more than anything.