That's exactly why it's at the top. If you enter "pu" and select your "Show pull requests" action a few times, you'll retrain Alfred to put that first.
You can tell Alfred to ignore AirPort Utility completely by adding the comment alfred:ignore to it (do a Get Info on the app in Finder). You can also reset Alfred’s “knowledge” in Alfred Preferences > Advanced > Clear Knowledge, but you’ll likely also lose a lot of training you’d rather keep.
More generally, it's not a good idea to blindly action things in Alfred without checking what's selected first. Alfred runs several different searches in parallel (one for apps, one for your workflows, one for contacts, one for files etc.), so its results aren't deterministic. If you've trained Alfred to associate "Show pull requests" with "pu", then that will always end up at the top of the results, but only after Alfred has finished searching. If one of the other searches finishes first, something else is going to be in the top spot until your preferred result comes in.
