Crocs are. For the most part very comfortable. There are medical versions which are a bit more supportive. I'd suggest that they are less likely to cause injury than the omnipresent flip-flop.
Not usually. No more than any other shoe. Your shoes need to be fit properly to your foot. Many people with foot problems find crocks to be comfortable and wide enough for their feet and to accomodate their foot problems.
Ankle and knee. The best protection is a good conditioning and strengthening program with knowledge of your limitations. Increase strengthening by 10% or so per week to limit stress injuries to bones and soft tissues. Some like bracing or taping, but very large studies show mostly placebo effects, unless specifically used to protect a known prior imbalance/injury. Read more...