Just activated old iPhone and App Store is trying to make me pay for an app I've already paid for I had an iPhone app on my iPhone 5s now currently under repair that had a $100 app called GIS kit.

I am connected to my iTunes account with the App Store, and have a bunch of apps that it's allowing me to download via the cloud download icon, but not this one.

So, a really quick way to answer this question would be with another question, and that is, does Apple even allow app creators to charge users twice for what is supposed to be a one time payment for an application?

I just activated this phone, have not done a hard reset or anything like that, so I'm hoping the GIS kit application simply just does not recognize that I have already downloaded it. But it could be something else, worst-case scenario I actually have to pay for it twice. Hope not.
No, Apple does not allow app creators to charge users twice for an app already purchased(in this context).
Of course the developer could create a new app with a new name, but identical content, and in that way try to get people to buy it twice. However that is not the case here.

Are you sure that you actually bought that program with that specific AppleID - are you sure you didn't buy it with a different ID?
You could check your purchasing history for your AppleID on iTunes (App Store).

Another thing to try is simply to press Download on the program, even though it doesn't display the Cloud symbol. If it downloads without requesting payment, you're good to go.