Why won't El Capitan run Homebrew after it has been successfully installed?
It's not clear to me what commands you actually entered into the Terminal, but based on the output, it looks like they were not entered correctly.

brew install upx

This is one command.  It instructs brew to install the command-line program upx.  It needs to be entered on its own line, after which you press enter.

upx -d "/Applications/Ableton Live 9 Suite.app/Contents/MacOS/Ableton Live 9 Suite"

This is the second command.  It tells the program upx to do something to the file at the path specified, with the -d option switch.  It assumes your Ableton installation exists on that exact path /Applications/Ableton Live 9 Suite.app/Contents/MacOS/Ableton Live 9 Suite with that exact name.  I'm not familiar with upx, so I assume that you're using the correct syntax for that program's execution.

The $ in the command you copied are shell prompts, and not part of the actual commands.