Just for the hell of it I started writing down the cost of each mission I sent my companions out on yesterday. On 25 missions ranging from level 5 to level 6 I lost money on 5 of them. I made right around 6k in profit without factoring in schematics or missions. While it is quite a bit lower then what it used to be it still brings in credits.
I realize my sample size is not very scientific so maybe I just had a string of luck, but to say you can't still make money on missions, at least in my humble opinion, appears to be wrong.