MK's neutral b should not really annoy or scare you, his quick aerials and fsmash should though.
No offense, but if you're fighting an MK and getting caught in his neutral B alot. You're being predictable and that's your main issue with it. Shield a lot, airdodge it, force him into blowing it early. Keep missile and zair pressure on him, both of those will make him blow it in an attempt to close in on you. Avoid it and punish him. The thing about Tornado is that, a direct hit on him from almost ANYTHING Samus has will cancel it, I've even canceled it with jab. Super missiles and low ftilts are the best for canceling it imo. He has to get in slightly close to be effective, anytime he uses it from a distance he's just asking to be punished as soon as it ends. Screw attack does more damage, is top tier priority wise and comes out faster. Use all of that to your advantage.
I'm going to kind of have to agree with Boolossus. Now it could be I haven't fought many very good MK's, but I think compared to the rest of the small members of the cast, he is one of the best match-ups for Samus. He's kind of floaty and semi-vulnerable to zair. Dtilt is WONDERFUL on him from my experience, it's great for starting combos on him due to his slightly floaty nature and size. Dmash is good on him also, as are both missiles. He's fairly easy to kill vertically, not so much horizontally. MK is also a fantastic edgeguarder, watch out for that. However, as a Samus, you should be giving him a ton of trouble in that category. Bomb jumping for mindgames and aerial dodging, tether, zair canceled AD, homing missiles all wreack havoc on an MK trying to edgeguard you due to his lack of projectiles. Your only real concern from an edgeguarding MK is his fsmash, that thing is freaking deadly, comes out EXTREMELY fast, and has high knockback. I've been finished by uncharged ones as low as 100%
Just take your time, MK isn't that big of an issue for Samus imo once you figure out how he works.