First, this doesn't seem to be an installation issue. You can try installing hisat2 using conda, which will give a more hassle-free installation.
Is the hisat2 folder in your PATH? If not, then just typing hisat2 -h would likely give you "command not found". I see in your first post that you used ./hisat2 while in the hisat2 folder, which worked fine. Does entering "./hisat2 -h" while in the hisat2 folder work?