Spammers are easy to deal with. Zoning is a different business and all players that zone will tell you that. I play a zoning game and basically the way to beat me is to figure out my patterns and find the holes (like a boss battle in any other game). When you are zoning and the other character comes through it's time to react. Try to bait a previous reaction. Maybe the last time you approached they rolled. This is a common strategy of less talented players that are spamming. Shoot shoot shoot roll. Try to bait the roll with an aerial approach. Land, and punish the roll instead of using the aerial. If they are shield grabbing your aerials, make sure you land behind them to remove this option (i.e. cross up aerials). If they use up b OoS (very good option for Samus), again, try to bait it, air dodge, then punish the lag.
You say you main villager. In your case, just put your damn tree up, spam loid yourself from inside the tree (where loid gets out but you are still protected from projectiles, and use pocket if they stupidly shoot their projectiles at your tree. Against Samus, a missile is probably just an attempt to fill up your pocket to follow up with a charge shot. Don't fill your pocket with a missile. CS can tank your missile and hit you. If they throw out a lot of missile CS combos, you can short hop the missile and fast fall to pocket the charged shot. This should make any samus very scared as it is generally a OHKO or a guaranteed shield break. TBH, villager is the toughest matchup for samus IMO.
Someone else mentioned zelda. When I play against a good zelda that is rough too. Her reflect lingers longer than it used to. Farore's wind is a legit attack that goes right through a zoning wall. If you are good at spacing Farore's wind you can definitely brutalize a zoning character unfamiliar with the matchup.
Finally, if you aren't any good with reflect characters and just try to bust them out and reflect, reflect, reflect, you will likely get badly punished by a zoner because they'll be able to bait your reflects and punish.