- you have way more packages on any Linux package manager.
- Linux package managers do not mess with /usr/local as expected in a UNIX compatible OS. Homebrew does. Linux package managers run as root, not in user-space.
- Apparently Homebrew gets broken by Apple software/OS updates.
- Linux package managers are an integral part of the OS environment and update process - it's structured this way even for critical system and kernel patches.
- Aptitude, for example, gets rid of older versions of packages, while Homebrew keeps all previous versions and simply changes the symlink. Cleanup is also automated in Linux package managers, not Homebrew as far as I know.
- Homebrew sometimes pulls up sources to compile software locally, while Linux distros usually pull up binaries (except AUR on Arch or Portage on Gentoo, or Sbopkg on Slackware). While compiling from source is nothing wrong, it can take a lot of time depending on what you are building.