I see you posted this question in june 2016. I started having the same problem around that time and it was after an update. In my case, I am in Mexico but was able set up apple pay using a US card. Before the update, Apple pay always showed up as a payment option in my iphone 6s, and I always used it to pay for my rides (even the ones in Mexico, where apple pay is not officially supported). After the update, apple pay disappeared while in Mexico, and to bring it back I came up with the following workaround: first, I logged in from uber.com instead of the app. While there, I checked my payment options and noticed apple pay was there and realized it was a location issue. So next thing, I changed my country from Mexico to the USA in my profile before logging off from the browser. From then on, all I need to do every time I open my app is log off and back on before I request any ride. That way, it will show apple pay as an option for at least long enough to be able to use it to pay for the ride before it is hidden again based on my location. So far, though cumbersome, it has worked for me every time. I haven't tried disabling location services for the app yet, to see if that permanently stops apple pay from disappearing. Based upon my experience, it appears that the update in June included the ability for uber to hide apple pay as a payment option (and perhaps other features), based on location, when using the app in an country that does not officially support it. Which is idiotic, because it's just one more credit card for all intents and purposes, so it doesn't matter, it will still work in any country. Now in your case, it also looks like uber hasn't updated the app to recognize Canada as an apple pay supporting country.
