The right to freedom of expression and opinions is a fundamental right as set out in Section 2of the Charter; the presumption of innocence is a right contained in Section 11 of the Charter which sets out the rights you have when you are charged with an offence and treatment within the judicial system as a result of such charge. It does not override fundamental rights of average citizens outside of the judicial system having an opinion:
from:
http://www.charterofrights.ca/en/16_00_02
The right to freedom of expression is not absolute, not is it always right. You have a right to say horribly racist things, but that doesn't mean that it is right, and asserting that it is your right to say racist things doesn't excuse the fact that by doing so you are denying other rights to other members of society. Not to say that you would say these things, just as an example. Everyone knows that freedom of expression does not allow for the yelling of "Fire!" in a crowded theatre, because it could cause harm to those inside who panic. I think that the point being made here is that people have the right to be presumed innocent and that right, like other human rights should extend to people outside of court as well, since everyone going around presuming someone is guilty because of what they have heard in the media, with no first hand knowledge themselves, can actually be harmful to someone because they cannot now get a fair trial, and will likely be found guilty even if they are innocent because of that prejudice given to the jury pool by the media and general gossip.
The courtrooms were traditionally the first places where racial discrimination was not tolerated, and now it is the norm to find the general public is no longer accustomed to denying anyone equal rights, perhaps some day in the future, people will take the right to be presumed innocent to the level of acceptance it deserves in society.