Bike lanes and paths, bike parking, and bike shops are needed for mere mortals to feel comfortable biking.

Being able to bike to lots of amenities should increase your Bike Score. Suggest calculating the Walk Score of the area you can bike to and factoring that into the Bike Score.

Steep hills should hurt the Bike Score of an area. I'd suggest analyzing the elevation gain/loss around the radius of a location. Maybe use 3.25 miles or a 15 minute bike ride.

The lower and slower, respectively, the better.

Seems similar to walkscore, but you need a way to identify (and hopefully weigh) good routes. It's not enough to have a few nearby lanes or paths, they need to actually connect you to the places you want to go (work, parks, businesses, etc.). Bonus points for nearby bike shops.

Ummm.... what other more direct indicator is there? Algorithms are helpful, but sampling of actual cycling is key.

Bicycle accident data could be used to come up with a bicycle safety rating for an area.

For some, a bikeable distance may only be 2 miles, while others are willing to ride 20 miles.

Even with a good grid of streets, it can be difficult to bike if major arterials do not have signalized crossing points.

Low, throughput and speed and high congestion and driver awareness are good for biking comfort and safety. The also tend to be the streets with the most enjoyable contexts.

Available bike parking is key to a successful bike friendly commercial district.

I find that unless you know an area really well it is really easy to get lost on a bike, especially if your are new to a town. Wayfinding signs are very helpful, good for marketing bicycle trips, and not expensive. Signs are a lot of bang for the buck.

Drivers and pedestrians who don't share well, cyclists who try to run down pedestrians or who weave in traffic, etc., all make cycling harder. How well do the police know and enforce local ordinances?

How many bikes are on the streets/paths vs the number of cars.

Use US Census data on bike-to-work mode share in the corresponding census district to estimate bikeability.