The reality is that we will likely never know what happened. In fact it's more likely that a theory will emerge in years to come and be presented as fact such as happened in the disappearance of Ben needham. 
.
IMO though one of the reasons why opinion turned against the family in the end was because of how things played out in the media. Bearing in mind that the media have a huge amount of influence over how people are viewed by the public, and this wasn't any less the case with the McCanns.
In the beginning there were searches, interviews, press statements, all very normal for the press. There was speculation as well, and Robert Murat was arrested iirc and practically hung drawn and quartered before being released without any kind of charge.
But what happened after that was odd. Not just in a "they didn't show emotions" kind of way, but out of the norm for any other case of its kind.
There was a fund. People started giving money, there were signs and posters all over the country, it was impossible not to know about this child's disappearance.
But more than that. The McCanns went to visit the pope. What for? And more to the point, they left their very small twins back in the very resort they claimed their daughter had been abducted from while they went to visit the pope to ... what exactly?
There was talk of what the money was going to be spent on, including paying the couple's mortgage on the house which the press hadn't wasted any time in telling the public how much it was worth. This was a well off couple accepting donations sometimes from elderly pensioners or people giving the last of their savings to pay their mortgage? Even though those people believed the payments were being made to help find Madeleine.
And Gerry McCann gave an interview just weeks after Madeleine disappeared talking about a potential concert to be given on the year anniversary of her disappearance. If they were looking for a living child, how could they be planning her one year anniversary?
Subsequent to that they have hired a spokes person, all paid for out of the Madeleine fund, and any discussion was quickly shut down with litigation being at the very top of their agenda.
The issue with all of this is that every single bit of it took away from what actually happened, people forgot that a child had disappeared, were told that they had to believe a certain theory or be sued, and the rest played out in the press like a soap opera.
It's impossible to know who made all that happen. Who set up the fund? Who suggested going to see the pope? How did the couple end up going along with all of this or was it all their idea?
And in the middle of it all a small child went missing, and her two siblings have no choice but to live in the shadow of that fact for the rest of their lives.