It is a real shame that we have to read the Scriptures through post-enlightenment, 21st century, western eyes. In our current context (though I think/hope the follow statement is less true everyday), doubt is something to be avoided. Thanks to the scientific method, we can know with near certainty about every minute detail of the world around us. To doubt is either to be too lazy to test a hypothesis or to be grasping at unprovable ideas.
But I don't think that was the case for Jesus' disciples. I think the doubt we hear about in Trinity Sunday's Gospel lesson was a holy doubt. The sort of doubt Jesus wished had been applied to some of the Pharisaical interpretations of Torah. The sort of doubt that takes it slow, listening, waiting, discerning between the Spirit of God and the rules of men. This doubt allows the disciples the chance to experience Jesus in all his majesty and mystery. This doubt is not a sign of weakness, but a beautiful engagement between human and divine.
We need to re-engage the ability to doubt, to allow folks to ask questions, to wait, to sit, to listen, to discern. It is not a weakness, a defect, but a chance to find God.