Why when I overlay a logo on top of the video, the white color part of the logo is transparent?
There is no white color. That's the background color of the page showing through. Your input PNG is palettized 8-bit image where black color indicates transparency.

Apply the following filter to the image to convert black pixels to white and set a uniform transparency.

geq=r='if(p(X,Y),p(X,Y),255)':g='if(p(X,Y),p(X,Y),255)':b='if(p(X,Y),p(X,Y),255)':a=0.1