Here's a nice informational post on the pitfalls of Blackboard as well as various Open Source and home-grown alternatives (including using blogs as an ad hoc course management system) from Kathleen Gilroy. The analogy I often make with Blackboard is to a classroom where all the seats are bolted to the floor. How the room is arranged matters. If students are going to be having a class discussion, maybe you put the chairs in a circle. If they will be doing groupwork, maybe you put them in groups. If they are doing lab work, you put them around lab tables. A good room set-up can't make a class succeed by itself, but a bad room set-up can make it fail. If there's a loud fan drowning out conversation or if the room is so hot that it's hard to concentrate, you will lose students.
A good CMS allows for flexibility in classroom set-up. For example, when I used dotLRN for a project (ironically, while working for Kathleen's company) I was able to meet with stakeholders and try different arrangements of the virtual chairs until we found one that they were comfortable with. The default set-up, which was optimised for on-campus students who took four or five courses at once and needed an aggregation portal, was completely unsuited for my audience, which was a group of full-time bond traders and other financial services people who were taking time out of their twelve-hour work days for one course. It wasn't worth their time to learn the complex (cluttered?) interface that made sense for a full-time college student. So we streamlined. We turned off functionality that we didn't need. We renamed pages to fit the students' expectations. We re-arranged portlet windows on pages and page order on the interface. We did all of this in 15 minutes without any programming.
In Blackboard, you can't do that. Sure, you can change the way the buttons look. And you can hide a button. But that's it. It's essentially only trivially configurable by the instructor. I strongly believe that this has a significant impact on distance learning drop-out rates.