iPhone Apps Backup?

Just "backed-up" my iPhone (as part of the Restore process recommended by Apple support in an attempt to fix a problem where Messages do not send.)

Didn't read the fine print: "...applications... will not be backed-up..."

Ergo, lost my password keeper app, ergo lost all my passwords, ergo pissed off!

Why aren't apps, pictures & songs backed up? By what rationale?

Who's to blame for this?