Clueless Aesop: The episode seems to be saying that while science and religion can co-exist they should always be separated. This ignores the fact that science and religion can co-exist peacefully, as evidenced by Gregor Mendel, the Friar who founded the scientific field of genetics, and the religious beliefs of the majority of Nobel laureates; something, Strawmanning aside, that would be difficult to fit in a half-hour episode.
At the end of the episode, Lisa tells Ned that she does respect his beliefs, but feels that science and religion should always be separated by way of telling him that she wouldn't want a scientist teaching religion anymore than she'd want a religious official teaching science.
Ned apologizing to Lisa for what he did and offering to take her out for ice cream along with his sons.
"Funny Aneurysm" Moment: The episode aired 2006, but consider the Tucson in 2011 happened at the shopping center, which killed 6 people and injuring 14 others including Gabrielle Giffords, who almost became the second in congress after Roy Ryan to die while in office. When ones looks at the scene where Snake was shooting at random at the Kwik-E-Mart.
Strawman Has a Point: While Ned does go too far, the museum's "Creationist" exhibit is needlessly insulting to people like him, and utterly unnecessary from a scientific standpoint. Had his complaint only focused on that, the writers would have had a much harder time pitting the audience against him.