Marth is a lot about pressure imo. He has a lot of tools at his disposal that shut us down. His sword easily takes care of missles and he has a counter that can eat a charge shot. Samus is tall, so it isn't that hard to hit her with Marth's quick aerials.
Zair is a GODSEND in this MU, but you have to know how to use it. When Marth dashes it puts him lower to the ground and makes it harder to zair or missle him, so, as poob said, will require some reading and predicting on your part.
I play a number of Marth's fairly often, a few are pretty decent, and they will almost always be on the offensive, so Samus has to go mega defensive.
An important factor to remember is that in order to use most of typical Marth playstyles involves short hopping aerials, especially fair.
OoS options are also very important in this MU. You should definitely throw out some Screw Attack before your opponent can start predicting it. If your oppnent is the kind that often uses 2 aerials in a SH an doesn't fastfall, SHZair is also an option.
Given Marth's recovery, most of the recover low to try to sweetspot the ledge. This is VERY bad for them because Samus can spike the straight out of the their UP-B. This can be risky however, because if you screw up the timing, and depending on the stage, you could get stage spiked.
Interesting note about facing Marth on BF, Marth has amazing platform pressure so be wary of that. Also, a number of Marth's like to plank the ledge by ledge dropping and fairing (Marth's fair goes through the stage and will hit you if you are near it), this is where i find the low CS very useful and can really catch them by surprise.
Overall, play defensive, observe your opponent, punish mistakes.
My bout is Disadvantage and i might goes as far as Heavy Disadvantage