Board Thread:Questions and Answers/@comment-98.242.202.188-20130614034909/@comment-1971498-20130614035530

In MGS1, it was hinted that it's only because Ocelot was mainly working in the shadows, and in doing so, was specifically ruled out from being targetted by FOXDIE.

In MGS4, I think it was hinted that because of how Ocelot was still supposedly working for the Partiots A.I., they didn't target him at all in MGS1 despite secretly plotting against them. It was only in MGS4 that they came to realize how dangerous his connection to them was (given how "Liquid" supposedly possessed him), thus deciding on finally offing him.