Why you use 'all is well' and not 'all are well'?

In this sense, "all" means "everything", which is singular. You say "all is well" just as you would say "everything is well."

In certain situations, "all" can refer to the members of a group and require a plural verb. For example, if a mother has given birth to quintuplets, and all five are healthy, you might say "all are well."