According to an article in the Canadian Cycling Magazine - no one really knows, but the leading speculation is that it represents the water of Canada, ie the Great Lakes, rivers, oceans:
The origin of the cycling blue is shrouded in mystery. [Kris Westwood] says that the colour is commonly thought to represent the many Canadian bodies of water, such as the Great Lakes and oceans. “Some say it specifically represents the three oceans our coastline touches,” he says. For a landlocked sport, water symbolism seems unexpected, but around the 1960s, when the first blue, red and white kits were released, Canada came very close to using a similar design for its new national flag.
The article also mentions that cycling isn't the only sport in which Canada diverts from the normal Red-White paring:
Many Canadian sports disciplines, such as track and field, have integrated black into their uniform design. Alpine skiing in Canada has often used a bright yellow in its design, Alpine Canada’s signature colour.
Though it would appear in these cases it is to distinguish from other countries with a similar Red-White colour scheme (for Skiing see: Denmark, Switzerland, Austria, Norway etc...)