"I just read the Canon post where the Avengers used the Mark II and EOS 7D to shoot several scenes, and in several other cinema movies. Why are all these movies using Canon and not Nikon?"
D800 was not out when they bought the camera gear :-) .. The Canon cameras did have an advantage over the nikon for a few years.. but the D7000 has more than caught up except for the lack of 60 fps.
The D800 has well and truly over taken the current crop of canon cameras .. but who knows what the next crop of canon cameras will be like.
check out this web series on video shooting with DSLRs note that it is a few years old now. http://www.zacuto.com/shootout