At this point trump needs tillerson way more than the tillerson needs trump.  Trump will for the time being accept the perceived insubordination.  

I read somewhere that tillerson took this job only reluctantly and didn't expect to stay more than a year.  He has boatloads of money and can get another position easily if he wants one.  He doesn't have an ideological axe to grind.  Add it all up and you have someone who can't be pushed around.