Supervenom

Protagonist necessarily doesn't have to be a Hero,take Lelouch or Light for examples even though they were the protagnoists of their own stories they were not 'Heroes'.

Or even Walter White from breaking Bad from a simple school teacher to a drug Kingpin.They all lack common heroic abilities which stops them from being a hero as we see in popular media in general. 

Eren follows the same character archetype 'The hero is always the protagonist (though the protagonist is not always a hero)'.

We started this story with Eren from a simple minded boy to where he is now and how his views have changed throughout the story.

Even though his actions are rather questionable now, from Eren's POV he thinks he is right he is fighting for his island and his friends which not wrong,because if it wasn't for Eren the island would've been doomed so in their eyes he is the 'Hero' 

We don't know what the future holds maybe he would save the world in his own way or destroy it or die in the process without achieving anything ,but whatever the case is he would always be the main protagonist of the story.