Well, I'm from Brazil, sorry for any spelling mistakes. This story is totally absurd for brazilians too, it's not a normal ocurrance for sure. This story sent chills on my spine the first time i've read... but saying that you'll avoid the country because of that is like avoiding to visit USA because of mass shootings in high schools... It's just those really sad brutalities that happen without a logical explanation and are not routine.
Like others have stated, this match was what we call a "pelada", it's a casual game between friends, family, neighbours. The ref probably was not a official one, maybe just someone from the neighborhood. The crime happened in a rural area, in a small town and normally there isn't much police force in places like these. When police arrived, it was too late. The crime is being investigated and one of the ref murderers is taken, the other are missing.
Brazil is also a very unequal country in terms of development. There are areas everywhere that are negleted, underdeveloped, missing a strong educational system and basic security. That's where violent crimes like those grow out of hand and gangs take over. Where the state commits violence against the people by negleting them a decent structure, violence is the answer. But I don't think that this explains this crime alone. The news aren't much clear, but it was just some individuals who really participated in the atrocities... and obviously, those involved clearly had some degree of psychopathy, including the referee, who started it all. Not justificating what happened, but the player was killed in front of his family and friends and it's hard to even imagine how people initially reacted to that, eventually escalating to the horrifying end. It wasn't a rational situation at all.
Unfortunatelly, it's true that is common to happen fights in soccer matches. My brother-in-law is a amateur goalie and he needed to run away from a finals game once because some crazy mob wanted to punch him after a ingame misunderstanding between him and a opposing player. This doesn't mean that people normally kill others after matches, tho, nor that every soccer game is violent. The international soccer games, for exemple, are way more family friendly because it's attended by people who like soccer more casually. People who doesn't have the patience or time to follow the brazilian league and just follow the national squad games, because it's pretty much part of the local culture, something to talk about at lunch time. Saying "did you see the national squad game yesterday?" is like a "the weather is good today, isn't?" in Brazil elevator talk.
Another point is that soccer is kind of a escape vault in Brazil and is mostly attended by low class people in the stadiums (rich people watches from TV)... and boy, the poor suffer in this country. You can live like in Europe if you have the money, or you can live in a favela if you don't. There's a lot of tension everywhere and a lot of misdirected anger from young people. Soccer clubs represent different classes... there's clubs that mostly represent lower class people, like Corinthians... or upper class, like São Paulo F.C... In my city, Campinas, there's a club called Ponte Preta, or "Black Bridge". The Black Bridge was where slaves were traded back in the days of slavery and it's the team that represents lower class people nowadays. Not surprisingly, their biggest rival is Guarani F.C, a team more attuned to upper class people in the city. There's always huge fights when they play against each other...
On national scale, the brazilian league is dominated by teams from São Paulo and Rio de Janeiro, the most developed states (waaay more developed that north and northeast states, which are always in the second division, struggling to keep at the first)
(Guess you can say that soccer violence in Brazil is something like a punk culture for some kids)
There's a lot of history in the founding of soccer clubs and that's why it's so important in our culture. Soccer represents our struggles as a country somehow. Not everyone is conscious of those histories, but team fandom and rivalries are generally passed from father to son, so history lingers on.