Is the flag Government sanctioned? If so it should fall under the separation of church and state but if they're led by Conservatives that won't mean a thing.
The thing is, "trust in God" --or more commonly, "in God we trust"-- is not in itself considered evidence of establishment of a religion. I always just mentally add the old punchline "... all others pay cash" and be done with worrying over whether some guy clerking in the convenience store assumes I'm religious when I hand him a dime.
If Trump is re-elected though I might start inspecting dimes to make sure they don't start saying that we trust in Trump.
It is kinda sneaky if Mississippi might be thinking about
telling people to trust in God on its new flag, instead of just assuming we already do.