Aquaporin and the exclusion of $H^+$
It doesn't matter where the $H^+$ comes from in the context of this information. The textbook is just saying that the aquaporin is permeable to $H_2O$ but not to $H_3O^+$ (nor, presumably, to $OH^-$).

In any aqueous solution, especially in the presence of acids, some of the molecules will be $H_3O^+$. The pH tells you how many. It doesn't really make sense to think about what a solution of $H_3O^+$ would look like.