Trusting certificates has changed on iOS 9. Before you could just "Trust" an installed app when tapping it open, however this function has now been moved into Settings.
How to:
Go to Settings
Go to General
Tap "Device Management" ("Profiles" in iOS 9.1)
Tap the dedicated enterprise company name.
Tap "Trust" and you're done!
Still can't figure it out?
Watch this video by OPERATIONiDROID on how to do this, step by step.