you're right of course, and the same thing happened (and continues to happen) to me; but then what happens? - zen doesn't leave us high and dry. Shunryu Suzuki says:
If you are seriously engaging this practice, and looking at your mind, and questioning the labels and beliefs and stories you lay on top of reality, you will start to doubt things you never doubted before.
Certainly happened to me.
So I read this as saying, yes, we start by 'realizing' our doubts - literally making them real - in zazen, so they become our reality (not a layer that we've laid somehow on top of something called 'reality') it's a revelation to us of what our labels, beliefs and stories actually are; but that's not the end of the story.
the purpose of studying buddhism is to to study ourselves and to forget ourselves. When we forget ourselves, we actually are the true activity of the big existence, or reality itself. When we realize this fact, there is no problem whatsoever in this world, and we can enjoy our life without feeling any difficulties. The purpose of our practice is to be aware of this fact.