Why do you think Kennedy lost popularity for supporting civil rights?

If we're talking about John F. Kennedy here, judging by the fact that he was assassinated on the year 1963, the same year Dr. Martin Luther King Jr. started his peaceful protests and the bus boycott. Hence why other racist people resented him, also the reason why he was assassinated by a white racist male named Lee Harvey Oswald, who resented black people.

(None of this was meant to be racist btw)