Anytime an author presents weather, it is typically not just rain, snow, wind, or sunshine; it is a message about the action of the storyline.
In this instance in chapter 5, rain can signify renewal of a relationship. It can wash away the past. It can cleanse what was wrong with the past so that the future can go on in purity. This rain happened in the middle of the day, and only for the time during which the meeting between Gatsby and Daisy was held. Had the rain been coupled with thunder and lightening or wind, it might signify a different change. In that case, it could foreshadow trouble. Here it's singular purpose is to demonstrate the birth of a relationship refreshed and cleansed. It is a little like a shower.