The presumption is that they are innocent. In order to be proven guilty, it must be beyond a reasonable doubt. Anything short of that standard, and we must assume they are not guilty. You are right though, that doesn't mean they didn't do what was alleged. It just means the crown couldn't meet the standard beyond a reasonable doubt. In addiiton, all the fact are not always admissable. That is where the nuance of the Criminal Justice system comes into play. A good lawyer, will make all kinds of arguments based on case law to argue inadmissibility of certain evidence. The majority of the criminal "legal" system is not about whether or not the person did something, it is about whether or not the crown can prove they did something, with the added pressure of arguing investigative actions or omissions, that investigators may or may not have done.
In any case, what is on trial is the accused rights, measured against the Charter of Rights and established case law.