What is a bootloader? At its most basic level, your Android smartphone is like a hard drive, made of up several partitions. One of those partitions holds the Android system files, another holds all the app data you accumulate (which is how you're usually able to update without losing all your stuff), and others to do more behind-the scenes stuff.
Think of the bootloader as a security checkpoint for all those partitions. Because if you're able to swap out what's on those partitions, you're able to break things if you don't know what you're doing. Or, with a little hackery, you're able to run custom ROMs.
There's a lot of squawking about bootloaders being "locked." Actually, most phones shipped with a "locked" bootloader, including the developer-friendly Nexus devices. (Nexus devices and a couple tablets are easily unlocked with a single command.) No, more accurately, most bootloaders are locked and encrypted, meaning the traditional "fastboot oem unlock" command won't do a thing.
And that's a bone of contention for those who love a manufacturer's hardware and want to tinker with their devices. HTC and Samsung and Motorola -- just about everyone, really -- ships devices with locked and/or encrypted bootloaders. Tinkerers (we really don't like calling 'em "hackers") have to find a way around the encryption, usually with some sort of an engineering bootloader that wasn't supposed to be available to the general public. But in recent months, we've seen HTC provide a free tool that will unlock the bootloaders on a number of its devices, and ASUS just got on board, too. Sony Ericsson recently has provided unlocking tools. Motorola's promised to do so as well, but there's been little movement. LG and Samsung ship with unencrypted bootloaders.
Why keep a bootloader out of reach? Probably the biggest reasons are that the carriers and manufacturers don't want to have to support hacked phones. The other is that a lot of time and money is spent developing these things. HTC Sense ain't cheap. Neither is TouchWiz. But Samsung and HTC both have managed to find a middle ground with the modding community, and pressure is on other companies to do so as well.