You can find detailed answer on your question here
Basically you need to add "-map" parameter to your command.
ffmpeg -i myMovie.mkv -c copy -map 0:v:0 -map 0:a:0 -map 0:s:0 myMovieMP4.mp4
-map 0:v:0
means, that you want to pick first video track from first input file "myMovie.mkv".
-map 0:a:0
means, that you want to pick first audio track from first input file "myMovie.mkv".
-map 0:s:0
means, that you want to pick first subtitles track from first input file "myMovie.mkv".
You can can input ffmpeg "myMovie.mkv" to look at the list of streams in the file.
This command with "-map 0" will put all available tracks into the output file:
ffmpeg -i input.mkv -map 0 -c:v libx264 -c:a aac -c:s mov_text output.mp4
Selecting streams with the -map option
To burn-in subtitles you can read the link at the top of the message or find another subject here at the stackexchange.
Basically you can burn-in subtitles from MKV to MP4 using this command
ffmpeg -i input.mkv -filter_complex "[0:v:0]subtitles=input.mkv:si=0[v]" `-map "[v]"` -map 0:a:0 -c:a copy output.mp4
[0:v:0]
- means, that you want to take first video stream from input file.
:si=0
- means, that you want to take first subtitle stream from input file
-map "[v]"
- means, that you want to put into your output video processed by filter_complex stream (video + subtitles).
-map 0:a:0
- means, that you want to take first audio stream from input file
Audio will be copied, video stream will be reencoded.
-c:v libx264
- reencode to x264