It is not always true that the automorphism group of an algebraic variety has a natural algebraic group structure. For example, the automorphism group of includes all the maps of the form where is any polynomial. I haven't thought through how to say this precisely in terms of functors, but this subgroup morally should be a connected infinite dimensional object, and is thus not a subobject of an algebraic group.
On the other hand, I believe that the automorphism group of a projective algebraic variety, , can be given the structure of algebraic group in a fairly natural way. This is something I've thought about myself, but not written down a careful proof nor found a reference for: For any automorphism of , consider the graph of as a subscheme of , and thus a point of the Hilbert scheme of . In this way, we get an embedding of point sets from into .
I believe that it should be easy to show that (1) is open in , and thus acquires a natural scheme structure and (2) composition of automorphisms is a map of schemes.
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