If you follow, unfollow, like or comment a thousand times a day over an extended period then your account will eventually be flagged and possibly suspended. There are many factors that determine how soon you get flagged, such as the age of your account, recent activity, previous flaggings as well as Instagram’s own secret algorithms. Try and keep your total actions per day under a few hundred and you will be fine.
If you perform certain actions faster than is possible for a human being then you will also get flagged. Therefore it is important to use a decent interval between each action to spread them out over a period of time. You can set this under Options -> Settings -> Time Delay. A setting of at least 1 minute is recommended. More will always be safer.