I don't think you were paying attention. It's one of the most radical and subversive mainstream films ever. How many Hollywood films do you know have a clear and direct argument for terrorism as a critical plot element?
you are joking right...
standard block buster 101:
anti hero appears isn't like the others is an outsider is ostracised alienated and seems to be doing things which destorys the status quo and challenges the system the system then bucks back to slap down the anti hero and show them to be errant and disorganised. once the anti hero conforms to the predesignated role they are destined to fill they become accepted and evevated in the society to be hearlded as a hero. roll credits...
now tell me again which holloywood films don't follow this set story line (not to mention that typcially when distilled to the boy meets girl blocking of actions or charchter development it could resonable be said that there are a only a few different cahrchter story archs retold in all hollywood films...)
more over there's nothing with in the matrix which tells you to go out and be an anti hero it neither takes the side of or against the anti hero... nor does it as you suggest promote terrorism....
it's genius if this can be said to be so is that it allows sufficent space for you and others to see all this type of ideas in it whislt actually being incredably conformist in it's narrative...
strip away the special effects and the mythology from the film the pretend faux subtext which is so shallow you couldn't drown in it and it's simply a hong kong action film set in the future with several main fights leading to the big boss end level charchter in a fairly pedestrian mumbo jumbo hokum manner in terms of story line...
(the second and thrid films cement this in place by providing fight scenes which are so pedestrain as to make you reach for the fast forward on the remote... i'm thinking neo vs smiths fight here... tea-de-oius...
the nonsense which is spouted by seemingly sensible people about these gash films is unbeleiveable...