A lot of people like to talk about Slytherins being poorly treated, and I'm not sure they were. Obviously there is an intense rivalry between Gryffindor and slytherin house that results in a lot of bullying that goes very much both ways, but that's the thing, it goes VERY much both ways. It definitely doesn't help Slytherin's reputation that the slytherin student we see the most of is Malfoy who goes to extreme lengths to be awful to Harry and the trio, and while they certainly get back at him on several occasions, nothing they do to him compares to his rather relentless crusade against them. We also see several examples of the Slytherin Quidditch team playing pretty dirty. There are a few games where the Gryffindor's pull to an early lead because of the Slytherin's committing numerous fouls (to the point where you really have to question the strategy. Its not only bad sportsmanship, but its costing them the game). While it is unlikely that Malfoy and the Quidditch team are entirely representative of Slytherin house, that is the side of the house we see, and its pretty nasty. Suffice to say though, there is tremendous animosity between Gryffindor and Slytherin house, and as much as we see crappy behavior from a lot of Slytherins, I wouldn't be surprised if there was also a lot of shitty behavior from some of the lesser seen Gryffindors.

Where it gets interesting is the other houses. I'm not entirely sure that the other two are as biased against Slytherin as seems to be widely believed (at least not until Voldemort's return). the other two houses seem to take a policy of cheering against whichever hosue has been doing the best for the longest. Yes, they seem eager to see Slytherin lose the house cup in the first book, but its said that this is because Slytherin has won it for many years in a row. By the time GoF comes around, Gryffindor has been on top for a few years, and people seem to sour significantly towards them especially after Harry becomes champion. Early in that book there is a lot of unity between Slytherin, Hufflepuff and Ravenclaw against the Gryffindors. We don't get to see as much of it, but it does seem there is an almost pendulum like effect with the other two houses, swinging away from whichever house has been dominating competitions recently.

Then we get into the issue of the Death Eaters. there are more children of death eaters in Slytherin house, than in any other house, and that is obviously going to hurt your reputation. While we, as adults, are able to look at how Harry paints that entire house with the same brush and determine that might not be entirely fair, I do think its understandable. He has not exactly had positive experiences with Slytherins, and while it is wrong to paint all of them as death eaters (just as it is wrong to paint all Muslims as terrorists), it is a very human reaction to what Harry has experienced. Harry is not perfect, and he makes an imperfect decision, but at the same time it is a realistic decision. I think the increased prejudice against Slytherin from the other houses at this time comes from much the same place, not justified, but realistic. And we do see older and wiser people like Dumbledore calling for unity, so we know this is not an attitude shared by all.

Beyond everything else I have said though, I think what it really comes down to is these are books, and more than that books aimed at a younger audience. While they convey some very serious and complex ideas, sometimes you need to create unrealistic situations for the sake of simplicity, and I think creating "A bad guy" house is one of those simplifications. It might not be realistic, and obviously not all real people who identify as Slytherin are going to be bad people, any more than people who identify as other houses would be all good people, it does seem to be very much the case that the majority of Slytherins in the books (At least during Harrys tenture) are "Bad guys"