First and foremost, the only way to be 100% about whether swine flu is covered on your travel insurance policy is to read the policy booklet or to contact the insurer in question. It may also be worth asking the insurer for confirmation in writing as to the terms on how swine flu is covered as most will only have general terms and conditions about medical conditions that were in place before the swine flu pandemic began.
This being said though, swine flu should be covered like any other medical condition. If any different, your insurer should have made you aware. On the assumption that your insurer is treating it like any other medical condition, as long as you did not contract the illness before the policy was taken out, you will be covered.
The cover will protect you against things such as not being able to travel due to being ill or being quarantined upon your arrival in other countries or having to receive medical treatment. All insurers are different though so, as mentioned earlier, check with your insurer to see what cover you do get but in most cases you will have something to compensate you if your holiday plans get ruined by this condition.