I can think of two possible reasons:

1) Website assets are generally optimized for size (images, etc.) and so reduce Cloudflare's total cost to service.

2) Cloudflare believes that free tier users who use it for their website assets are more likely to want the other Cloudflare services and therefore convert to paying customers.

For example CloudFlare's free tier is not intended to be free transit or storage for other services that are substantially about selling storage and transit. If you make an image-processing CDN type thing, like imgix, CloudFlare does not intend to subsidize almost all of your costs.