You need to specify the path to the tools-builder folder, which is where ctags is. Try this:
arduino-builder \
-compile \
-hardware /usr/share/arduino/hardware \
-tools /usr/share/arduino/hardware/tools \
-tools /usr/share/arduino/tools-builder \
-libraries lib \
-fqbn arduino:avr:uno \
-build-path .build \
src/main.ino