It’s worth remembering that it is fundamentally unnatural for a human to be up in the air.
What you’re feeling is the body’s normal response to a perceived danger. The three best strategies for overcoming this fear are:
1. Rational analysis (which is what you are doing already);
2. Knowledge of the theory and mechanics of flight and the risk management that should form an integral part of flight training. This can be accomplished through self-study and instructor briefings; and
3. Experience, for which there is no shortcut!
Everyone will overcome their fears and concerns at their own pace. Dont worry if you never lose these feelings completely: they may save your life one day!