Before I begin, I want to say loud and clear that the majority of Yugioh players are good people.  I've made a few very close friends through the game and have met lots of great people through the game.  Unfortunately, the community has many bad apples too. 

Yugioh and its players in general tend to get a bad reputation relative to other card games.   

Problems 

Some people see collectible card games as inherently nerdy, but Yugioh tends to get the most hate.  While it was cool in middle school, many of us duelists hid our cards in high school because it was frowned upon.  Magic the Gathering was acceptable though.  Where I grew up, other card game players frowned upon Yugioh players but, to some degree, I now understand their reasons. 

Numerous comic book store owners have told me that the Yugioh crowd has caused more problems for them than the other 5 card/board games they hosted combined, between the constant swearing, the stealing, the loud arguments, gambling, the cheating and the messes they leave behind.  I don't doubt that.  Some said they wouldn't host Yugioh if not for the fact that it was their most profitable game.  The owner of the comic book store I most frequented eventually got fed up with all of the problems, had a meltdown, and yelled at the Yugioh players ; duelists stopped coming and the 

But why is the Yugioh crowd like this? 

Adolescence 

The vast majority of Yugioh players are 15 to 25 year old males (you could say the same thing about 4Chan).  If you put them together in a big room for 6 hours, it can possibly become like Lord of the Flies by William Golding.  In the book, a bunch of boys are stranded on an island and they regress into savage behavior.  It also becomes like high school, with cliques and outcasts, except the tournament organizers and store owners aren't teachers or counselers ; it wasn't their obligation to protect us.   

It is unfair to the many good people who play the game to be instantly lumped into one category of stigma. But even if 1/3 of the players are immature and brutish, it can poison the entire atmosphere and drive the good people away.  

Bullying 

When I was 13, I was bullied a lot by other Yugioh players, punched, threatened to be beat up on the street, the list goes on.  It didn't help that I used to be chubby, socially awkward and had big crooked teeth, but I doubt the Pokemon community would have treated me that way.  Over 5 years of puberty, I gained a foot of height, 50 lbs, some muscle and better social skills.  People were nicer to me, but the Yugioh community was still, on average, very immature. 

Look at the Pojo forums for example: the Magic and Pokemon sections are generally fine, but the mods are constantly banning cyberbullies in the Yugioh section. 

Bullying is unfortunately tolerated in many places because the good players would see the disrespect but not speak out against it.  They just want to play the game – not get involved in controversy.  They're the silent majority. 

Diverse Demographics 

I think the reason why other card games have a better reputation and less problems is because they have a more diverse group of players.  The Pokemon crowd for example: 5-10 year old kids play it, as well as their parents and their older brother ; a fair amount of women play it too.  As a result, it's a zone where brutish behavior and disrespect won't be tolerated at all.  Magic the Gathering, being an original classic, draws in older crowds.  Men in their late 20's, 30's and 40's have long outgrown teenage antics and won't tolerate them either. 

As I wrote in an older article for this site, the violent and sexual card arts appeal to the hormonal teenagers – not so much to women.  The overall lore and atmosphere Yugioh itself hase been too cartoony for most older adults and perhaps a little too dark and racy for little kids. 

We Can Fix This Problem 

It's been a long time since the game's infancy.  The game had four additional television series' and over a hundred different sets by now.  I'd be surprised if half of the current player base was around in 2003.  We can erase the board, and draw in new demographics if we want to, but it's not a coincidence that we're often looked down upon.