The answer to this question will depend entirely on your opinion and what you feel is the book's true message. After going through a severe ordeal, being ridiculed, harassed, isolated, and finally beaten, Jerry has proven something about himself and he has had something proven to him as well.
In his last appearance in the book, Jerry attempts to tell Goober to follow along.
When The Goober leans over him, Jerry wants to tell him to play ball, to play by the rules, and not to go out on a limb, not to try and disturb the universe. But Jerry cannot speak.
Having learned the potential price for stubborn individuality, Jerry wants to tell Goober:
"They tell you to do your thing, but they don't mean it. They don't want you to do your thing, not unless it's their thing too."
If you feel that Jerry is justified in advising Goober to fit in and to try not to stand out, then you will agree with Jerry's idea that Goober should play football. That is what is expected of him.
If you feel that Jerry is upset when he conceives of this advice and that it goes against the message of the book, then you will not agree that Goober should follow along. If the book's message is related to ideas of personal strength and positive notions of independence and individuality, Jerry's advice serves as a counterpoint to the novel.
One of the most interesting things about this book is the passage in question here. After so much investment and sacrifice made for the cause of standing up for himself, Jerry expresses the idea that the outcome was not worth the effort; not worth the cost.
Yet, a great majority of the novel seems to side with the validity of Jerry's enterprise. He is, after all, the hero. Though he does not win the fight, he is not beaten into agreement or submission to the will of others. He succeeds beyond everyone's expectations.
What then is the final comment being made? Like the answer to the question you've posed, the final interpretation is going to be up to you.