First run a Forced Verify to make sure all your internal files are correct. Once that's done trying logging in. If it still doesn't work try disabling your Firewall before you log on to see if something in the Firewall is blocking access to the launcher since the new patch. Sometimes new patches change the pathing routes and to routes your Firewall doesn't recognize and blocks them.
I'd also run a TraceRt and Nettest to make certain there's not a problem between you and Cryptic's servers that's not allowing you to log in.
STO is about my Liberated Borg Federation Captain with his Breen 1st Officer, Jem'Hadar Tactical Officer, Liberated Borg Engineering Officer, Android Ops Officer, Photonic Science Officer, Gorn Science Officer, and Reman Medical Officer jumping into their Jem'Hadar Carrier and flying off to do missions for the new Romulan Empire. But for some players allowing a T5 Connie to be used breaks the canon in the game.
Comments
I'd also run a TraceRt and Nettest to make certain there's not a problem between you and Cryptic's servers that's not allowing you to log in.