Perhaps I am overlooking the obvious, but I cannot find an answer to this question: if the subjunctive is used to express uncertainty, why is every question in Spanish not in the subjunctive, as the uncertainty is inherent until the question is answered?
The subjunctive is used in modern Spanish virtually exclusively in subordinate clauses.1 For this reason, the main clause of any question is in the indicative.
However, what you're thinking about does come into play with certain types of questions where subjunctive would not be allowed in the declarative counterpart:
- ¿Crees que exista Dios?
— Sí, creo que existe.
— No, no creo que exista.
This is because at the moment of uttering, we don't yet know whether you believe it or not. Now, compare this to a similar question
- ¿Crees que existe Dios?
The difference is that we're not asking if you do or do not believe in God, so much as questioning the whole statement and analogous to English's "You believe in God?" (compared to the first one that is the more canonical "Do you believe in God?").
1. In the Spanish of not that long ago, the subjunctive could be used much more freely on its own. Nowadays, that use is almost entirely relegated to exhortative commands (¡Coma Vd.!, ¡Comamos!) and all other uses are generally preceded with a que: que sea fácil el exámen which emphasizes the subordinate structure, versus older sea fácil el exámen.