As someone who was a Star Trek fan and not a B5 fan in the 90s I have to say I think I may know why B5 fans and Star Trek fans don't get along and part of it may be our fault. That is not to say that there are not B5 fans who are not jerks but I had on e friend when I was a kid who was a B5 fan and the rest were Star Trek fans and remembering how we used to treat him does not make me proud. heck years later when I went online for the first time i remember how myself and other Star Trek fans used to troll B5 message boards and make really personal attacks against JMS and some of the actors. I remember that we used to mock everything about B5,from the CGI,to the actors,and we even used to accuse B5 of stealing all their ideas from Star trek. Heck i remember a petition being started to try and get production stopped on the B5 computer game(Sadly the game was never released for other reasons)on the grounds that if it had space ship in it and an alliance of planets then it was ripped off of Star Trek. I am ashamed to say I signed that one.
Of course years latter I learned about how Paramount was the first place JMS pitched B5 and how he showed them the series bible and some of his early ideas ended up in Star Trek movies and episodes after they turned him down. Now has he stirred the pot since,sure. Is it the fault of Star Trek fans that the studio did that? No. Still I think that caused him and the fans to become very defensive and I would be lying if I said I didn't understand why. I think the fans got tired of always having to defend their favorite show so they started going on the attack to try and drive Star Trek fans away,and soon you couldn't be a fan of both shows. That is a shame because now that I have seen both shows years latter I can say they are nothing alike and there is room in my heart for both shows.
As for why Star Trek fans did it? I can only say that I think we were all scared. We were used to Star Trek being top dog and getting all the praise and then all of the sudden out of nowhere this little upstart show came that was enough like Star Trek that it was in directly competing in Star Tek's main medium. Yeah we had had Star Wars before but that was a one hundred percent different type of story and it was movies and Star Trek was on TV,by the time Star Trek got really popular in movie theaters Star Wars was onto it's last movie so we didn't really have to worry about Star Wars stealing anything from Star trek. Then all of the sudden this new show with a strong fan base and lots of buzz from critics came along on TV,while Star Trek was airing! It seemed like there was a chance it could beat Star Trek and if Star Trek was beat would that mean the end of the franchise?! I think a lot of us assumed the worst without ever seeing more then a picture of a Centuria and without watching an episode of the show we decided that this show was a cheap silly knock off that was trying to force Star Trek off of the air and when the writer said some negative things about Star Trek that just confirmed it. Star Trek always had a strong fan base that defended the show and we sprung into action to take down the imposter and save Star Trek. It seems silly now but as I recall that is how I am a lot of others felt and in trying to save star trek we destroyed any chance of the two fan bases getting along.
Were there faults on both sides? Yes there sure were I knew some B5 fans online who could be very mean. Still as a Star Trek fan i have to say myself and others bare a large portion of blame for creating a rift that sadly exists to this day.