This echoes some of the other answers, but I wanted to weigh in:
Flesh them out
Create an actual NPC village exactly the same way you would create one of a non-monstrous race. Create villages, shops, story arcs, government, etc.
At the humanoid village
Try to keep most of the "crimes" of the monstrous race to be non-specific. Have the villagers say things like "there's one that I caught stalking my daughter!" (reality: they both happened to go to the river for water at the same time). Maybe give one actual issue that people keep citing but upon deeper reflection most of the other "stories" are really misinterpretations or outright racism.
Do not create random encounters
The party's first encounter with this group (I'll say lizardfolk from now on but obviously whichever race you choose), won't be "okay now the PCs are going to meet 5 random lizardfolk, rolled from XYZ table with ABC treasure", but it will be "the village has patrolling guards." They will act like guards do. They won't attack unless attacked first, they may be interested in why the party is there and ask them questions, but they won't attempt to detain the party unless the party gives them cause.
If you really want to create an effect where "they seem hostile at first, but the party begins to slowly realize..." you can create a "crime" for the party to commit by accident. For example, if the party trespasses in someone's farm or, worse, an egg creche, without realizing it, then the guards will try to arrest (but not kill) the party, and the party, expecting combat, attempts to fight back.
The guards, when some of them are killed, the rest would probably flee rather than fight to the death. Flesh out their inventory with things that guards might normally have, like whistles, standardized weapons and uniforms, etc.
Have the local government respond the way a lawful good government would
If this is the beginning of the campaign, the party will almost certainly not be able to overwhelm an entire large, organized settlement. The reason that civilizations go the organized route is that it keeps the people alive and conserves resources (as opposed to the chaotic evil that constantly wastes resources fighting each other). If it's one town, there will still probably be some people that are higher level. They may eventually capture the party and give them a trial and counsel and the party may realize that it's not a sham trial, and that "oh crap, we just killed some people with families etc. what have we done?"
Take charge, respectfully
Treat your players' action declarations as statements of intent rather than a completed part of the narrative. Feel free to slow things down to insert details and intermediate steps when needed. What they are doing isn't always a problem. When a player says:
"Ok, I go there."
...treat what they said as:
"Ok, I intend to go there."
You don't need to scold the player for jumping the gun, just narrate the next thing that's important to your story.
Player: "Ok, I go there."
GM: "Great. You set off on the vaguely stone-paved path towards..."
Sometimes, there won't be anything in the middle and "going there" is a reasonable shortcut to the next part of the story.
Skipping to the Good Stuff
Your players can't read minds, and don't know that you have some cool encounter planned for halfway through the journey. From what they know, getting to the destination is the next short-term goal they have, and the endpoint holds the next thing worth stopping for. It's natural for them to set their sights there, and try to do it directly. We normally skip over things like eating, sleeping, and an uneventful walk down a familiar street.
When there's something worth stopping for, it's the GM's turn to say so. Don't worry about asking people to "hold on". Confidently narrate the next thing you want to focus on, and the player(s) will follow along with your story. If they don't, then they are trying to jump ahead and away from you, and you can tell them directly that things don't work that way.
Shortcutting Out of a Scene
You're in the middle of talking to the blacksmith. He describes a mission. After the description, the player says "Ok, I go there."
The problem here isn't that they skipped the mid-travel encounter. The problem is that they abruptly and prematurely ended a scene that you were roleplaying through with them. It makes the narrative feel choppy and disconnected.
It can be OK to short-cut through some of the details to wrap the scene up quickly, but only after the purpose of the scene has been resolved. The purpose of this scene was to tell the Rogue about the mission, and have her agree (or not, it's up to her) to do it. Think of a book or a movie. A scene might cut after the hero says "I'm the man for the job", because we can skip the details of him having more smalltalk with the smith and walking out of the shop. The scene won't normally cut immediately after the mission is described, because it feels unresolved.
When a player cuts ahead like this, you should ask them to wait or slow down a little. They should know better. With practice, they eventually will.
Blacksmith: "...and bring the rune stone back to me. I'll pay you $300."
Player: "Ok, I go there."
GM: "Wait, what? The blacksmith has asked something of you, and made an offer. What do you say to him?"
Point out the incongruity ("Wait, what?"), and then put the player back into the important part of the narrative.
Best Answer
Give consumable items that go away on their own.
I speak as one of the players who will absolutely hoard every potion they get forever, and try to sell them in town for gear upgrades. So your characters want to hang onto their potions? Okay. Cool. Let them. Introduce a new type of consumable item - mushrooms or something. Every time you take a long rest, you roll a d6 for each one, and the mushrooms that get a 6 stop being useful. This forcibly breaks the idea that those items have any sort of long-term hoarding value, and no one in town really wants to buy the things because in a week they'll be useless anyway. Have mushrooms grow in high-magic areas (like the places that you'll often have to fight monsters) and basically duplicate potions. Possibly have the occasional herbalist in town who sells them for cheaper than the alchemist sells potions, but still won't buy the things, because if the party doesn't want them, she has no one to sell them to.
Once you utterly break the idea that the consumables can be seen in any way as a long-term resource, people will start using them as the short-term resource that they're intended to be... and those same urges to not waste will bite them every time they roll a six during a long rest, encouraging them further not to hoard. In the meantime, they don't have a reason to feel cheated because you're not taking anything away. They still have the potions they've earned, they can hoard them all they like, and they can even buy more. It's always easier to give a new thing than to take an old thing away.
I admit that I haven't been in a game where this was tried, but it would totally work on me. This answer refined from part of an earlier answer by Quadratic Wizard.