The main problem here is naming, because I don't think there's an English word that means "set whether this thing is enabled or disabled." Maybe there is, and if you can come up with one, I think a combined function would be OK. If it's clear that "not enabled" is the same as "disabled" then setEnabled is an OK function name.
Another consideration is whether you typically have a boolean already that indicates the desired state (e.g. from a config file), or whether you work out whether to enable or disable this thing based on more complicated logic. If it's the former, and you have to do this in several places, maybe the convenience of being able to just do setEnabled(flag) beats having to do if (flag) { enable(); } else { disable(); }.