With iOS 10.3 Apple changed the mechanism for trusting a self-signed certificate. Before you simply just send the PEM file to your phone and it would install as a profile and the certificate would be trusted. Now that's no longer the case as even after installing the certificate, the cert is not trusted.
Even when I use Apple Configurator to make a profile that trusts my cert, it still doesn't behave as trusted on the system.
How do I trust a self-signed certificate in iOS 10.3?