I searched the Tripadvisor Israel forum and found this thread that mentioned that this app automatically gives you the lowest possible fare so if you ride enough times in a day to make the day pass worthwhile, it just charges you the day pass rate. That sounds fantastic (and is confirmed here on their official site).

I also played with the app a bit and it looks like we should be able to get my son the youth rate, although I need to wait until we arrive in Israel as we have to upload a photo of his visa that he won't get until we arrive.

So this app seems way better than the card so long as we keep our phones charged and have local data plans.