No single root cause, but I'd say a combination of rapid growth, a changing market with no obvious (at-the-time) answers, some resource issues, and some missteps by some people.
The company began to grow fast in the years after I joined. VMware's early culture was amazing (a template for any company, imho), but it's hard to maintain that with fast growth. Not a unique situation, but I feel it had an impact on how we addressed certain challenges.
ESX was big, and we wanted to figure out the next big thing. There were a few initiatives, some gambles. Reorgs didn't always match and some initiatives got starved, others over-fed.
Let me take the opportunity to say that we did have a lot of freedom in engineering to build and experiment, which I always loved. This was a strength of the company. Personally, I got to figure out and build Unity in our Workstation product (it let you pop windws out of a VM into the host -- SUPER challenging), the whole remote VM infrastructure for Workstation (took 3 years with a major rewrite), WSX (early-days HTML5 client for accessing VMs using just a native browser and a network connection), amongst others.
But the world changed and we didn't really nail this. Case in point, The Cloud. (And later Docker.)
In early Cloud days, we were trying to figure out what that all this really should look like, how we fit in. We had things in the works that didn't get released or got restarted, we had some really useful bits that got spun out. What we should have built was more obvious in retrospect, but not so much at the time.
I think we had a lot of really good people in the management chain, and overall people were trying to do the right things there. But we did have a few high-impact bone-headed decisions (some short-term cost savings at the expense of longer-term strategy in parts of some departments) and some people who shouldn't have had the responsibilities they did (in my opinion). Some of these decisions may have made sense at those levels at the time due to factors they were dealing with that I don't know about, but these did damage.
Bear in mind, it was a big company in a quickly-evolving industry, and it's not always easy to get things right. I would NOT say "corporate greed" or "screwing over customers" or anything like that. Not while I was there. But missteps and hard questions to answer about the future.
All that said, I enjoyed working there. I left to work on Review Board (https://www.reviewboard.org) full time in 2013, and then my old team disbanded in 2016, but much of the team still gets dinner every month, 10 years later. Still sees movies, still hangs out in a Discord. I wouldn't trade working there for anything.