Taken from a Quora post written by Ken Weinstein, Red Line captain 2003.
Let’s start with some history: the team adopted the Red Line  name before the 2000-2001 season. Prior names included Odysceus (????-1993), Harvard Disciples (1993-1995), and the Dukes of Harvard (1995-2000).
Throughout my freshman year, the 1999-2000 season, there were occasional discussions of changing the team’s name. While the program had experienced its greatest success as the Dukes, making its first trip to nationals in 1998, the name simply wasn’t made to last. The TV show on which the name punned went off the air in 1985, so while it may have been a touchstone in the youth of team leaders like Doug Moore ‘98, freshmen in the new millennium remembered it only from reruns, if at all. Moreover, by failing to conform to the [college name] [team name] format, it inevitably led to confusion. People called us the Harvard Dukes, which killed the pun and sounded stupid, especially when we played Duke. By the spring of 2000, the Dukes name was almost vestigial; we referred to ourselves much more often as HMF.
So why not HMF as a team name? (After all, Carleton has had a long and successful history with the simple acronym CUT.) Among other reasons, in its PG interpretation the F stands for Frisbee, a trademark that, somewhat ridiculously, is no longer officially part of the sport’s name. We play Ultimate (yup, just an adjective) and we throw a disc. I really wish Wham-O and Discraft had sorted all this out years ago. Some believe the sport is destined to someday be known as flatball, in which case HMF would’ve been prescient, but even so there is no official men’s division, only “open”. Don’t ask.
A lot of terrible ideas were brainstormed during long car rides – I seem to remember someone furiously advocating for Jelly or Peanut Butter and Jelly at one point – and I don’t know of any reasonable contenders that came up other than Red Line. I believe that Sam Stake ’03 originally suggested the name during a track workout. There was no formal team vote, but I don’t know of any serious protest when the rising captains (Dave Kallin ’01-‘02 and Adam “Skippy” Ross ’02) announced the name change prior to the start of the fall 2000 season.
Why has the name stuck? It’s simple, it fits well in cheers like “I believe in Red Line” and R-E-D-Line, and it works on many levels in both goofy and serious ways, from a reference to the local subway line (shared with rivals Tufts and MIT but claimed for our own) to the traditional team color plus line as Ultimate jargon for the seven players on the field, to high-RPM/high-intensity play. Also, it naturally gave rise to BRed Line, an oustanding B-team name. With six nationals appearances in 11 years as the Red Line and George Stubbs ’11 as the program’s first ever Callahan (national MVP) winner, it seems unlikely the name, now imbued with a history of success, will change anytime soon.
 The spring 2000 jerseys made no mention of Dukes beyond an “01″ reference to the General Lee, but did have an HMF logo: http://kendrickkay.net/de
 I’m proud to take full credit for that one, along with the immortal “No Soup for You” cheer.
 The only scenario in which I could imagine a change is if Ultimate became an NCAA sport, and Harvard required the team to use the Crimson name, logo, and colors.