Another reason is that , in addition to the large number of undocumented workers that cross this border, there is also a large amount of illegal and dangerous substances. A substantial trafficking business in illegal narcotics, guns and even human trafficking of slaves and prostitutes takes place with far greater frequency on the southern border of the US as opposed to the Canadian one.
Increasingly since 9/11, the Canadian border is receiving more attention from customs and Border Patrol agents, but it is unlikely that it will ever receive as much focus as the US - Mexico border.
I would say that the major reason for this is that Mexico has historically been a much less stable country than Canada. In addition, the major flow of illegal immigration has been through Mexico and not through Canada. For these reasons, it is logical that that border should get more scrutiny than the northern border.
Of course, you can argue that there are racial reasons for this, if you are so inclined. There is definitely racial animosity on the part of some Americans towards Mexicans.
However, I think that even without this animosity, there would be more scrutiny of Mexico. Partly because of Mexico's lack of stability and prosperity (and partly due to the fact that Central and South America lie to the south of Mexico) Mexico has been a conduit for drugs and illegal immigrants. Because of this, it is natural to worry about other things, such as terrorists, coming through there.