There are many examples to suggest Simon Birch is a virtuous character. First, and probably most obviously, is Simon Birch's utter and complete sense of faith in God and God's plan for his life. It is a running theme throughout the movie, supported by several scenes and several lines. When teased about his size, Simon Birch is unfazed. He knows there is a reason he survived birth and a reason he is different from other kids. His sense of confidence in this (his faith, essentially) is evident in his lack of reaction to teasing and peer pressure, and in his conversations with Joe, which reveal him to have a maturity well beyond his age.
There are also several scenes in which Simon speaks out against the message that is taught in his very traditional but not necessarily practical church. In one scene, the reverend of the church is asking for God's help for a church fundraiser. Simon Birch responds, aloud (though not loudly), "I doubt if God is interested in our church activities. If God has made the bake sale a priority, we're all in a lot of trouble." This isn't his only nugget of wisdom when it comes to church action versus church belief versus church message. Simon Birch is clearly frustrated that the church has almost lost the meaning of true faith and connection to a God he himself, clearly feels very connected to.
Finally, the climactic scene of the bus full of children sliding into the river is an example of Simon Birch putting others lives before his own. When the bus driver abandons everyone and swims to safety, Simon Birch sacrificially calms down and then leads the children out of the bus, and must dive down to help one get out because his foot is stuck. The scene ends with the bus sinking and the possibility that Simon Birch does not make it out alive. Though he does make it out of the bus, we know he dies soon after (likely due to the length of time he spent in frigid water).
As a 12 year old boy, he jokes coarsely, curses, and talks openly of things only 12 year old boys talk about. One of the beauties of this movie is that the title character is exactly as believable as he is unbelievable. But is Simon Birch virtuous? In many unexpected ways, the answer to this question is yes.