During the first few weeks of fall you can ride with just toe covers over your cycling shoes (I prefer the Planet Bike Dasher Windproof Toe Covers). However, as the temperature drops a bit your next line of defense is going to be a lightweight shoe cover that will not only protect your toes but your ankles as well.
The Louis Garneau Wind Dry SL Shoe Cover is not only windproof and very breathable. This product is made with laminated Lycra and fleece on the inside with a WindDry fabric on the outside. These covers are not waterproof (though some advertisements make that claim), but I have found them to be fairly warm in temperatures down to around 35 degrees. The back of the cover closes with a sturdy strip of Velcro and there is a Velcro fastener under the sole the works well at keeping the cover in place.
I used this cover on my road shoes last year and was very happy with it. Reinforced cleat openings on the bottom of this cover make it compatible with most pedal systems (I use Look Keo cleats). There are also lug openings in case you want to use this cover on your MTB shoes. You will also find a decent amount of reflective tape and logos that should help motorists see you easier.
This is a decent shoe cover and I really don’t have any complaints against it. However, it is not intended to replace winter cycling boots, or even heavyweight thermal shoe covers. There are several good lightweight shoe covers available and I think most people would be happy with this one.
The Louis Garneau Wind Dry SL Shoe Cover retails for around $35 and is available in four sizes: X-Small (36-38), Small (39-41), Medium (41.5-43), Large (43.5-45), and XL (45.5-50).