I greatly admire Jane Fonda. The Vietnam War was indeed a huge mistake and it was because of people like Jane Fonda that made this abundantly clear - influencing huge numbers of students (like myself at the time) to do something to stop it. If she pissed people off in the process, so be it. She was right.
However, I believe both Jane and Peter had some issues with their father that were not solely due to their political views, but I believe fences were mended towards the end - with Jane appearing with her father in the film On Golden Pond - Henry Fonda’s last film, if I am not mistaken.