In my humble opinion, blackboard and the like (moodle, sakai...) are mainly useful for core classes that have a lot of students taking quizzes or writing papers or doing readings.
Faculty and instructors, I think, sometimes forget when they have academic freedom to teach their course whatever way they see best (sometimes they really don't have this choice though, like for much government/military/corporate training). They can use stuff outside of blackboard if they wish. Also though, they may not have the time or skill to set up their own online course tools.
There are alternatives that many faculty are embracing such as wikis (wikispaces, etc.), blogs (wordpress), and even some universities are exploring more decentralized or cloud-based alternatives that don't box you into a walled garden, like wordpress hosting, drupal tools (harvard's openscholar), google apps, and see what BYU is creating (although I'm not sensing that it will be open sourced): http://learningsuite.byu.edu/ (described in the educause article below)
The newest LMS tools like Instructure (and the newest version of Blackboard) are basically trying to emulate Facebook, for better and for worse, with dynamic streams of information and connections to social networking tools. Some believe Blackboard will not dominate the market for much longer: http://mfeldstein.com/emerging-trends-in-lms-ed-tech-market/
Anyway, there are plenty of articles exploring the effects (negative and otherwise) of learning management systems like Blackboard: http://www.educause.edu/EDUCAUSE+Quarterly/EDUCAUSEQuarterly...
http://firstmonday.org/htbin/cgiwrap/bin/ojs/index.php/fm/ar...
http://firstmonday.org/htbin/cgiwrap/bin/ojs/index.php/fm/ar...
Unfortunately many academic IT departments are primarily just consumers of vendor technologies, they aren't big enough nor do they have enough money to develop custom software tools. Purdue and others are some exceptions: http://campustechnology.com/innovators
An even bigger problem is probably that most faculty have no training in instruction and pedagogy and learning theory and design. As one person put it, "College teaching may be the only skilled profession for which systematic training is neither required nor provided–pizza delivery jobs come with more instruction." See http://edtechdev.wordpress.com/2009/08/31/50-examples-of-the...