Analog and RF circuits are laid out completely by hand! But there are often a lot of symmetries and repeated structures that mean you can re-use a lot of layout. Also, designs are often copied, reused, and repurposed, so those layouts just get modified to adjust, which saves time.

For large digital circuits (e.g. CPUs), it's all automated. There's a lot of human involvement, but ultimately a computer is placing all the transistors and wiring them together.