So, let's discuss the first example...
Society does not have the right to protect itself from dangerous individuals. Individuals have the right to this. In order to achieve these goals, individuals have empowered their government to protect their right to life and property.
Any scenario in which society is defending itself against an individual A can probably be reduced to one where society is the agent of one individual B defending themselves against A, I'll give you that. This is not always clear-cut, however: it may be a question of a contradiction between A and B's rights, for instance in the commonly-cited example of yelling fire in a theater. If you view things as it being purely about the individual, how do you resolve this kind of conflict? Why is A's right to free speech less important than B's right to life? You probably can't get them to agree, but if it's all down to the individual, then society has no right to step in and resolve the discussion for them.
But, more importantly, I don't think it makes sense to define things so narrowly. Society can be reduced to its individuals because in the end it's solely composed of and defined by a collection individuals. But in a similar vein, a person is only composed of cells, so why do we speak about the rights of a person and not of individual cells? What's so special about the particular level of organization that corresponds to one individual human? Society - Human - Cell - Chemical... each is an ordered cooperative of lower elements, so what makes human the unique one that deserves rights above all others?
To put it differently, I don't believe in inalienable rights, for the same reason that I don't believe in absolutes. I think the set of rights the US has is a very good one, but I wouldn't be so presumptuous as to call them the truth, the best, or the everlasting.
Same argument applies to any of the examples we're discussing.