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    Welcome on SuperUser. It seems that mp4 does not support alpha channel... Give it a look. BTW edit your post adding the command you used to convert from MOV I to WebM and that worked. It can be useful for others...
    – Hastur
    Commented Feb 12, 2021 at 11:57
  • VP9 can support alpha, and you can put that in MP4, but I'm not sure what's what you want or if your browser will support it. Anyway, I can't give you an answer you can blindly copy and paste without seeing info about your input as provided by ffmpeg -i input.mov.
    – llogan
    Commented Feb 12, 2021 at 21:46