If you're going to have a day at school to raise awareness about harassment toward gay, lesbian, bisexual and transgender people, then it's dodgy to try and suppress dissenting political speech about the matter, like a shirt. I can see the school's initial reaction, and even possibly applaud the sentiment behind it, but I think it did represent a suppression of political speech.
This case is also worth noting as a demonstration of how the characterization of the ACLU as a "liberal" organization is so often off the mark. It's not a liberal (or conservative) organization. It fights for the rights of people of any political persuasion or belief to be heard. It's just that, more often than not, it's conservative / traditional authorities that have tried to keep a lid on dissenting speech, thus making it seem like the ACLU is just out to fight for liberal causes. They are not, as this case clearly shows.
Reshared post from +Les Jenkins
If speech is free then it must protect unpopular as well as popular speech.
Connecticut School Backs Down; Permits Anti-Gay Shirt
The ACLU and the school regard it as free speech.
The lawyer for the school district this month wrote to the American Civil Liberties Union of Connecticut, saying Wolcott High School student Seth Groody may wear the T-shirt, which bears a slash mark through a rainbow. The other side showed a male and female stick figure holding hands above the message “Excessive Speech Day,” the ACLU of Connecticut said.
The ACLU said Groody wore the shirt April …

Good. Now everyone knows that kid is an asshole.
Or, at the very least, ignorant. Some of the nicest people I know are also some of the most ignorant. They hold the beliefs they do mainly because it is what they were taught to believe.
I believe in the right of people to be stupid… I just wish they didn't exercise it so damn often.