In most countries it's extremely hard to formally get anyone convicted of murder (or manslaughter) if you don't have a corpse to point to; even if you have the corpse but the parts where the killing act "kicked in" are missing (as when a body has been dismembered and spread about) it can be impossible. So the case doesn't go to court: to get someone convicted you want hard forensic evidence. Most courts also like to see a weapon that's supposed to have been used.
Still, I think the police are justified in working on the assumption that the parents may have been involved in their daughter's death/disappearance. So many murders are committed by friends, family or next-of-kin, and the longer she's gone withoiut anything really to support the idea that she's been abducted, the more it becomes viable to look for other paths. Naming someone as a suspect is a formal thing of course, something you don't do unless you have some kind of idea of what happened and some "soft evidence" but the case doesn't have to be complete and watertight at the moment when they are named. Anyone will see that the parents are not being named as guilty at this point, before anything has even gone to court, and if it does go to court, it's a totally safe bet there will be several rounds.
No one has to look upon the couple as "the definite killers" but the trouble is that the media, when writing about crimes, scandals and suspect crimes will often rely so heavily on the police and the prosecutors or - in this case - on somebody who has been a part of the story all along. No one can deny the media to write about what they get, but you'd hope they could at least evaluate what they wrote after a while and take a hard look: is this an interesting story? are we doing a good job here? is anything even happening here?
In the two months or so before the police singled out the parents as suspects, almost nothing happened except for stuff that the McCanns and the media generated by themselves: Beckham, the visit to the Pope, a number of claimed "sightings of Madeline" and a lot of interviews. The story snowballed, but nothing was happening. I really think it's unsound reporting, and honestly I dislike it for the same reason that I'm not very fond of excessive conspiracy writing about big disasters: it lives off a boil of sensationalized feelings.