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Here's a question; does tying up someone count as "rope use"? When is something a skill check?
You gain a +2 trait bonus on skill checks involving climbing and rope use, and a +4 trait bonus on Appraise checks to determine the value of large quantities of bulk goods without opening their containers.
http://www.d20pfsrd.com/traits/regional-traits/wharf-rat
If you have your target pinned, otherwise restrained, or unconscious, you can use rope to tie him up. This works like a pin effect, but the DC to escape the bonds is equal to 20 + your Combat Maneuver Bonus (instead of your CMD). The ropes do not need to make a check every round to maintain the pin. If you are grappling the target, you can attempt to tie him up in ropes, but doing so requires a combat maneuver check at a –10 penalty. If the DC to escape from these bindings is higher than 20 + the target's CMB, the target cannot escape from the bonds, even with a natural 20 on the check.
A skill check would be something rolled on Climb or some other particular, defined skill. Tying someone up is certainly rope use, but it does not invoke any of the skills, just your CMB, so it is not a skill check.
Tying someone up is a combat maneuver, not a skill check.
So no, Wharf Rat definitely will not apply as it only apply to skill checks involving rope.