Lois can interbreed with Superman in Superman Returns.
Does that mean Superman is a subspecies of Homo Sapien?
Answer
http://en.wikipedia.org/wiki/Man_of_Steel,_Woman_of_Kleenex details the actual problems the two would have to overcome during sexual intercourse.
http://www.rawbw.com/~svw/superman.html is the actual text.
To summarise: it ain't gonna happen.
But that doesn't answer the question whether Kryptonians and humans are the same species. Of course being able to interbreed (which Niven states isn't possible) doesn't mean the two are of the same species. Interspecies crossbreeding is often performed in order to create hybrids between species. All it requires is a high enough level of genetic similarity between the species, which usually indicates a common ancestor not too far down the inheritance tree (e.g. a lion and a tiger afaik can be bred together, despite being different species).
So if the movie is correct in postulating that cross breeding the two is possible (despite the counter arguments as to the actual problems of performing such an act as presented by Niven), all we can ascertain is that they have a relatively recent common ancestor (which could hint at panspermia, the idea that life on different planets originates at the same point).
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