Fence lines
I have looked at YYZ site maps, and as far as I can tell (some of the maps are a little hard to interpret), the aircraft would have crossed unpaved ground, then the 'South Service Road', then the primary security line fence, then more open ground, then the public road leading to the Infield Cargo Area (and Control Tower and other facilities), then stopped in the ravine.
There would be about 250 m of cross-country travel (i.e., 250 m if the ground were level) required to cross the distance between the freeway (Highway 401) and the crash site, and yes, there should be a chain-link fence at the edge of the airport property -- but this would be a 'non-security fence'. The public road inside the airport property would have been much closer, but would have much less traffic than the 401.
I suppose those people who did cross that outer fence got over it or through it the usual way -- they climbed it. I emphasize again that this would not have been the primary security line fence, since it was separating the highway right-of-way from a publicly-accessible portion of the airport property, so this may not have been too difficult for the physically-fit and adrenaline-charged.