I created my own CA certificate on Mac, imported it to an iPad and had the same issue with not seeing it in the "Certificate Trust Settings". Turned out I was importing a .p12 file instead of a .cer file (both are available as export from the Mac Keychain app). The Configuration Profile under Settings > General > VPN & Device Management looks absolutely identical in both cases! BUT it doesn't show up to be trusted in Settings > About > Certificate Trust Settings if the .p12 file was used!