Why are McGonagall, Hagrid and Flitwick allowed to stay at Hogwarts after Voldemort took power

Why indeed?

McGonagall and Hagrid are active members of the Order of the Phoenix. Flitwick is not but is obviously affiliated with them. Same goes for the other teachers - while they are not members, they surely sympathize with the cause and will take sides against Voldemort if they have to choose. Hagrid has to flee but just after he hosts the "Support Harry Potter" party.

It could be argued that Hogwarts is not of tactical importance (at least not short term) but keeping quite powerful wizards free is not quite wise.

In general most of the Order of the Phoenix seem to be ignored or just monitored rather than actively chased and arrested. The Weaslyes have to hide under the Fidelius charm but only after time.

So instead of eliminating the threat with a lightning strike for example by detaining the guests at the wedding they let them some time to regroup and go undercover.