Weakness has nothing to do with whether or not two elements amplify each other. It has to do more with the fact that both chakra natures are coming from the same side (either the same person or allies).
Some elements' weaknesses work by the "stronger" element canceling out the "weaker" one (e.g. water canceling out fire). Others work by the "weaker" amplifying the "stronger" one (e.g. lightning amplifying water, wind amplifying fire).
However, if one person (kekkei genkai/two chakra natures) or two allies (cooperation jutsu) are using a technique, the chakra will generally combine to create a stronger technique (because energy will be released even if two elements cancel each other). For example, ice style = water + wind, and vapor style = water + fire. This is similar in that Naruto's wind style is augmenting the impact force of the water via a cooperation jutsu.