Bdtyk

I learned that the boot loader is permanently stored in the machine's ROM and today’s PCs is constructed with flash memory technology so it could be altered under special circumstances.

Is rm -rf / is the special circumstance?

Does rm -rf remove the boot loader?

TL;DR: rm -rf / doesn't remove bootloader itself, but everything that bootloader needs (and everything OS needs to function).

boot loader is permanently stored in the machine's ROM

Not quite. On most modern systems, bootloader can be either on Master Boot Record part of the disk - the first 512 B - or it can be on separate device (see also). And to quote Wikipedia about linux kernel image:

...limitations on some i386 systems meant only the first 1024 cylinders of the hard disk were addressable.

To overcome this, Linux distributors encouraged users to create a partition at the beginning of their drives specifically for storing bootloader and kernel related files.

Embedded systems, such as Raspberry Pi, may in fact have a bootloader (or first stage bootloader) in ROM.

rm -rf / like any other command is loaded in memory and executed from there, so it removes recursively everything in / directory (/ filesystem), including its own original file /bin/rm. It generally knows nothing about MBR partition and operates only on all files/directories that can be found under /.

In other words, the first 512 B of disk that have the bootloader itself aren't removed, but /boot directory is removed, and that does contain configuration files for bootloader (typically GRUB) and temporary filesystem initrd.img which is loaded before the main / filesystem. If you look at the Grub rescue article on linux.com, you'll see that even though bootloader itself might be working, it has to know the disk on which root filesystem is located, where kernel image vmlinuz is located, and initrd. That is, the example they give in grub's shell is

grub> set root=(hd0,1)

grub> linux /boot/vmlinuz-3.13.0-29-generic root=/dev/sda1

grub> initrd /boot/initrd.img-3.13.0-29-generic

grub> boot

where (hd0,1) identifies disk and partition with root filesystem.

Even though bootloader itself is not removed, when /boot alone is removed that does lead to problems. In case of rm -rf / you are removing everything from filesystem, including init - the very first process, the kernel