It kind of sounds like they just wanted to make it easier for students to not fail, but I'll take a stab at arguing for making 50 the lowest grade.
On any given assignment in most classes, especially ones with more subjective grading, around 50% of the possible points are essentially for participation. It doesn't really make that much sense, if we want to give grades to students based on how well we think they understand the material, to give students a worse grade for simply not turning something in than for turning something in that reveals that they have no idea what they're doing.
Examples:
There are multiple-choice tests in science or history classes where the expected grade given totally random guessing is still 25%. It doesn't take any real mastery of the subject to eliminate one to two choices on a typical question, so getting half of the questions right is achievable even if a student is actually incredibly ignorant. Edit: Hell, I remember true/false assignments and even tests with substantial true/false components.
Essays that are turned in are basically graded on a 50-100 scale, or an even more restrictive one. You just don't see grades of 10 or 20 on essays even when they fail as essays in virtually every way imaginable. Having occasionally seen samples of undergraduate writing, I know for a fact that students are passing high school English courses without being able to put together a coherent paragraph.
So the idea is that zeros are just an arbitrarily worse grade than failing miserably - it takes a lot more good work after a zero to dig out of that hole than it takes to recover from "only" failing miserably, and it's not obvious why "didn't show up" deserves so much worse of a grade than "doesn't understand the subject at all".