I mean, like hurricanes, meteors, volcanic eruptions, etc.? Perhaps the protection of Hogwarts can withstand strong wind (I'm not sure) but what about volcanoes? And what about meteors?
Signs point to “no”
I don’t think we can reach any conclusions with complete certainty, but the evidence suggests not:
Hogwarts is not protected against natural low temperatures:
The skies and the ceiling of the Great Hall turned a pale, pearly gray, the mountains around Hogwarts became snowcapped, and the temperature in the castle dropped so far that many students wore their thick protective dragon skin gloves in the corridors between lessons.
Harry Potter and the Order of the Phoenix
It doesn’t appear to be safe from breezes, either:
The start of December brought wind and sleet to Hogwarts. Drafty though the castle always was in winter, Harry was glad of its fires and thick walls every time he passed the Durmstrang ship on the lake, which was pitching in the high winds, its black sails billowing against the dark skies.
Harry Potter and the Goblet of Fire
That the castle is “drafty” suggests that cold air is coming in from the outside.
It would seem that the only protection Hogwarts has from ordinary atmospheric conditions is that which is normal for a building of its size and materials.
It’s also perhaps worth noting that the protections around the castle put up no resistance to having a large object (Hagrid) hurled through a window:
Lost in desperate speculation, Harry turned a corner, but he had taken only a few steps down the new corridor when the window to his left broke open with a deafening, shattering crash. As he leapt aside, a gigantic body flew in through the window and hit the opposite wall. Something large and furry detached itself, whimpering, from the new arrival and flung itself at Harry.
Harry Potter and the Deathly Hallows
Now, is it possible that Hogwarts is protected from more violent natural phenomena (as opposed to magical attacks)? Is it possible, for example, that while the protections would not prevent Hagrid from being thrown through a window, they would deflect a meteor? Is it possible that while they did not protect against winter weather, they would repel the heat of lava?
Certainly, but I don’t believe we’ve seen any evidence to suggest this is the case.
It’s also worth noting that:
Meteor strikes, though they can occur in Scotland as much as anywhere else, are very rare events (per area).
Hurricanes (or at least winds of similar strength) have occurred in Scotland in the past, but are not at all common. Besides, such conditions hardly present much of a threat to individuals capable of Apparition, since they tend to come on gradually.