Yes, I have developed such irrational fears and loss of confidence, but not in relation to flying. My cure was to see the situation for what it was - an irrational fear, but this took alot of time (more than necessary I felt)
You are part way there already - you understand the problem and can describe it, and you know it is irrational.
Unfortunately with any 'dangerous sport', there is always an basis of truth in the fear you feel. Flying is not as safe as driving a car. It is easy to allow the heightened sense of risk that follows a close call to become over-exaggerated - to the point there it forms the basis of an irrational fear.
Try to hook into the good feelings that you have had from Flying in the past, and try to see the actual risk involved accurately.