Some Arduino projects doesn’t need and USB connectivity. In most cases it is only needed to program the Arduino and then it becomes a redundant part which takes place on board. If you find this problematic then choose different Arduino board versions without USB. All you need is to connect a serial converter once to program and then use minimal board to run the project.
Without USB, an Arudino becomes a bit cheaper, simpler and smaller. Without this part it becomes easy to build it on prototyping board. Anyway you will need at least one USB to serial adapter in order to upload sketch to chip. Hans likes to keep everything minimal in his projects. If project doesn’t need USB then he won’t choose overloaded boards for it. And he thought also to make a minimal USB to serial Arduino programmer. It’s even non FT232RL bases, but FT230x which is a bit different but it seems that AVRdude doesn’t have problem with it. Programmer is so small that it doesn’t have an USB connector – connector is designed directly on PCB. Interface chip is in QFN package which is a bit tricky to solder.