I read this article and shrugged. I've been hanging out in academic departments in a few specialties for awhile now, and at the end of the day, you could probably take "MD Anderson" and replace it with "Your Institution's".
The reality is that as research funding gets poorer and clinical reimbursements decline, institutions are squeezed to produce more revenue. There is also an increasing administrative bureaucracy stemming from a number of sources such as regulation. So this manifests itself in a number of ways.
1) The clinical faculty are pressed to see more patients for the same salary.
This may manifest as incentivizing faculty to be more clinically productive by providing bonuses for RVUs. It may also manifest as giving RVU or other minimums to keep your base salary or your job. This can create some wacky scenarios where certain subspecialties within radiation oncology work very hard to generate their RVUs, while others can generate RVUs much more easily. All of these things create resentment.
In the private practice world, this may have be completely true. "Hey, IMRT took a hit this past year, so now we need to see 10% more patients to keep up our salary." They understand and work around these scenarios. The academic physicians tend to be more divorced from these economic realities.
2) The research faculty are pressed to find funding.
In an environment where research funding is tight, start-up resources and packages are scarce. Institutional funding is scarce. Why does the institution want to invest in high paid physician-scientists (or for that matter, research oriented residents...) who often fail/run off to private practice when there is a glut of PhD-only types who are willing to do infinite post-doc work for $50k/year.
In any case, how the limited research money gets distributed is a constant source of conflict. The primary clinical faculty get angry they have to work harder for less salary, while part of a research faculty's salary or experimental funding comes from the institution. The clinicians often view this as a tax to be in academics.
Meanwhile, the researchers often find the institution's allotments arbitrary, because in reality they are. This means if your administration is friendly towards you or your type of work, hooray! If not, get ready to be upset or leave.
3) The administration is expanding and is often non-clinical.
The overhead for running institutions has been exploding over the past decade, in part because hospital based care pays better and the money gets distributed in odd ways, and in part because the regulations for hospital based care has been expanding. A lot of specialty talent outside of medicine is brought in to provide administration, marketing, IT support, billing, etc...
So in the end, you have a lot of MBAs running hospitals these days. They may not understand the situations from our perspective. They may not even run things fairly, instead focusing on the bottom line and seeing physicians as "providers" and patients as "clients" or "customers". As a result, a lot of institutions are implementing higher target revenue goals for clinical faculty, even as the institution remains profitable. This creates instant resentment as well.
In the end, residents are often not made aware of these conflicts. Medical students are completely clueless--professing their love of "academics" while having no idea about the actual real world of medicine.
The reality is that within academics you will find a lot of people who feel that they are working clinically at private practice levels, with minimal support for research, and with much less salary than they could be making in private practice. This seems to me to be the vast majority of modern academic positions. For the salaries from the AAMC survey (post #11 above), this paragraph applies to those positions.
Faculty stay in these positions for a lot of various reasons. Some are tied to a specific location and the academic job is the only availability in that tight market, some really hate the private world due to dislike of practice management (guess who complains when these issues hit the academic world...) or have personalities that don't get them referrals in the private world, while others really do enjoy certain things about academics like a high level of support staff (such as residents) or the ability (with all the caveats above) to run a research lab or clinical trials. In today's world, that last group of people seem very scarce (if you think it might be you, see:
http://forums.studentdoctor.net/showpost.php?p=13356317&postcount=4). When you're talking about the small minority of serious research based positions in academics, as gfunk points out, you are looking more at the salaries for "instructor" level, and the salaries below (even well below) the 25th percentiles in the AAMC survey, unless you have finally made it to be at the level of a big name chair.
