Hogwarts has a very different threat profile to regular schools. It faces a lot of security challenges and risks that aren’t usually relevant. This mandates additional security measures that don’t or can’t apply to a Muggle school.
Let’s break down some of the additional protections:
Muggle-repelling charms. When Professor Binns is telling the history of Hogwarts, he says:
“You all know, of course, that Hogwarts was founded over a thousand years ago — the precise date is uncertain — by the four greatest witches and wizards of the age. The four school Houses are named after them: Godric Gryffindor, Helga Hufflepuff, Rowena Ravenclaw, and Salazar Slytherin. They built this castle together, far from prying Muggle eyes, for it was an age when magic was feared by common people, and witches and wizards suffered much persecution.”
— Chamber of Secrets, chapter 9 (The Writing on the Wall)
This remains an issue in the present day. This is not a problem for Muggle schools, who usually want as many people as possible to have seen and heard of them.
Unplottability. When discussing foreign schools, Hermione explains:
“There’s traditionally been a lot of rivalry between all the magic schools. Durmstrang and Beauxbatons like to conceal their whereabouts so nobody can steal their secrets.”
— Goblet of Fire, chapter 11 (Aboard the Hogwarts Express)
Hogwarts has lots of unusual magic – the Room of Requirement, the moving staircases, the ceiling in the Great Hall – that might be of interest to third parties. Unplottability makes it harder for these people to find the castle.
Ban on apparition and a controlled Floo network. Allow people outside the castle to apparate in or enter via Floo is a massive security hole. It’s very likely this would give direct access to student areas, such as dormitories or houses. You can understand why people would be nervous about allowing this degree of access.
Teleportation does not exist and therefore is not a threat to regular schools. Simple border protections (“a guard on the door”) are enough to keep out ne’er-do-wells. That doesn’t work if somebody can go straight past the border guard.
Internal apparition is bad for students. Okay, so you’re not allowed to appartate in. Could you apparate out? Or around the castle?
Apparating out is verboten because it would allow students to leave the castle without permission (more on that shortly).
Apparating around is dangerous, because an inexperienced student could easily splinch and do themselves a serious injury. That’s why it’s only allowed under carefully controlled and monitored circumstances, such as the apparition lessons. It would also be a rule-breaker’s dream, because they can get away from the scene of a crime in seconds. Imagine the pranks you could pull with instant teleportation.
Restricting student movement. This one isn’t so unusual. Hogwarts is a boarding school, and a lot of boarding schools impose similar restrictions on students leaving the school. Quoting from the Wikipedia article:
Pupils generally need permission to go outside defined school bounds; they may be allowed to travel off-campus at certain times.
Edit: Fine, let’s address dark wizards as well. There are – and have always been, and probably always will be – nefarious actors in the magical community. No different to the Muggle world.
Hogwarts is the bottleneck for British magical education, which would make it a big target for dark wizards. Plenty of reasons for this:
All the children of significant people go here. Whether you’re an Auror, or politician, or senior banker at Gringotts, whoever – if your children are magical, they go to Hogwarts. Kidnapping or hurting Hogwarts students would be an easy way to get lots of political leverage.
In the Muggle world, children of Prime Ministers or Presidents often get enhanced security at school. The magical world is no different, except it’s provided by default because there’s such a concentration of targetable children.
Pretty much every magical child in Britain goes through Hogwarts. Killing chunks of the student population would dry up the pipeline for future Aurors and Ministry officials.
Spectacle. I don’t think Hogwarts has ever been successfully taken by an attacker (the end of Deathly Hallows maybe?), which makes it a more tempting target. Imagine the fear you’d instill if you captured Hogwarts – that’s got to count for something.