I've been feeling for some time that the way the parents stayed in Portugal and publicized the case from there, this long after, spoke against them. When nothing seems to be happening for three or four months, why would one stay and try very clearly, by press conferences and enlisting celebrities, to give the impression that it must be a kidnapping and that the girl wasn't dead? It kind of smacks of pressurizing the police and, at the same time, showing a version of the story where the McCanns could not be questioned.
Hundreds of kids disappear in strange circumstances every year in Western Europe or in the USA, but I don't ever recall a case that's made the headlines like this for such a long time - being from Sweden I'm uncomfortably reminded of the series of press briefings conducted by the Police chief of Stockholm, Mr Hans Holmér, in 1986-87 after the assassination of PM Olof Palme. Holmér enthralled journalists from all over Europe by speaking in a semi-poetic language ("preminiscent" of Donald Rumsfeld) of the difficult mission and of what might soon be happening but there was no real hard progress; the case is still not closed though some would say it's "police-wise solved without a chance of getting the /now dead/ presumed assassin to justice".
I wouldn't believe the mother is an intentional killer, but she probably knows what happened and like wingsofanangel said, you wouldn't leave a child of that age alone in a hotel room in a strange city