Unfortunately, swan parents will try to kill their own young if they know the cygnets are in distress or something is wrong with them. The male may have tried to get the cygnet out of the weeds and found out that he could not facilitate the rescue, so killing the cygnet was much better than having it suffer.

Since, you rescued the little one, the parents took it back and everything should be fine. This near drowning in the weeds may have been what caused the other cygnets to meet their demise. The Regal Swan