What is boot protocol and why should I be concerned?
"Boot protocol" mode is a stripped down subset of USB HID (the overarching standard for USB "Human Interface Devices" like keyboards, mice, joysticks, gamepads, etc.) designed to make it easy to support keyboards and mice with very limited code in the BIOS. This was very important back before operating systems had widespread support for USB, and it's still sometimes needed in order for the keyboard to be usable in the "BIOS setup" type screens, though some new BIOSes and EFI systems include full HID support. Windows 95 OSR2 also only supported this mode, but every OS since Windows 98 (though somewhat limited), including Windows 2000 and newer, has had full HID support.
This mode has a limitation of 6 simultaneous keypresses on keyboards. If you exceed 6 simultaneous keys pressed, the keyboard will indicate "rollover".
It is not REQUIRED that all keyboards run in this mode, but most conventional keyboards do so that they have maximal compatibility. The USB HID standard clearly intended for almost all keyboards to implement alternate settings that would remove the 6-key limitation, but in practice no cheap keyboard does, and it would require special "drivers" on Windows to support switching to that mode, anyway. Some high-end keyboards, like Das Keyboard, get around this by having a special hotkey sequence to toggle between boot protocol mode and a mode with no (or a very high) limit on simultaneous keypresses. Most arcade encoder boards using specialized firmware, rather than off-the-shelf keyboard controller silicon, never run in this mode, since rarely does anybody want to us Windows 95 OSR2 or set up their PC's BIOS settings using their arcade control panel.
Support for an arbitrary number of simultaneous keypresses is commonly called "Full N-key Rollover". Contrary to what seems to be somewhat common belief, this is fully possible with USB, but you do have to give up boot protocol mode to do it.
Super annoyingly, a lot of PS/2 to USB adapters not only are restricted to boot protocol mode (and hence 6 simultaneous keypresses), they also cancel all active keys after some lengthy-but-easily-encountered period. This makes them unsuitable for gaming.
There is a similar "boot protocol" mouse profile. This is not so common these days, since it has an arbitrary limitation on the number of buttons and axes that many common gaming mice, etc. exceed, and nobody really cares about having mouse support when running their BIOS setup. It was mostly important for a couple years where USB mice were starting to become popular (supplanting PS/2 and serial mice) but OS support hadn't caught up yet. In those cases, the BIOS emulated a PS/2 mouse in software, and generally it only supported the boot protocol mode.