Harvard just isn't top tier in either computer science or electrical engineering, or any tech-heavy engineering field you can think of, really. This article manages to spew a bunch of nonsense about incubators while ignoring that fact. What they call "even humble University of Washington" is a top-10 CS school, and Harvard is not.
For what it's worth, Cornell is the only Ivy League school amongst the top-10 for CS.
That said, there is still a strong reason to consider a private university (even if they are not in the top 10 for CS, but are still amongst the top 25). Many of the flag ship state universities do not directly admit students to the CS department. CS major is considered "impacted", and admission criteria may have very little to do with programming ability (e.g., UW CSE emphasizes grades in Physics and Math).
OTOH, I believe you can still transfer into the UC Berkeley BA CS program -- in the College of Arts and Letters from a community college with ~3.6-3.8 GPA. Transferring or getting admitted into the BS EECS program (in the school of engineering) is much harder, but the CS classes the students take are no different. The "BA" vs. "BS" means very little at Berkeley, as they also grant BAs in Physics/Math/etc...
If you're intrinsically motivated and are fairly set on being a software engineer or going to grad school in CS (as opposed to also pondering electrical/computer engineering), going to a community college which is considered a feeder school for Berkeley (such as De Anza College) and transferring into the BA CS program at Berkeley/UCLA/UCSD/UCSC seems to be route of least resistance.
Of course the big downsides are losing the first 2-3 years of the social "college experience" (important if you're more interested in entrepreneurship rather than being an individual contributor) as well as limited internship opportunities during freshman/sophomore years (OTOH participating in open source or doing side projects will help greatly).
 It can take up 3 or more years to transfer due to lack of space in many general education and major pre-requisite classes: I was unable to register in a vector calculus class until sophomore year just due to supply/demand and lack of registration priority.
Princeton gets on some top 10 lists as well. But the point isn't that there's anything wrong with Harvard or the Ivies in general (you'll surely get a fine CS education at Harvard, Cornell, Princeton, Brown, Columbia, Penn, maybe even Yale), the point is that the center of gravity in the tech startup world is right now at the schools with top-tier CS and Engineering departments, and it's not because they have some special "incubator" sauce that other universities don't, it's just that they attract a large body of entrepreneurially-focused students.
It's the same issue with comparing MBA programs to accelerator programs. A Masters in Business Administration is NOT a Masters in Entrepreneurship, which I would argue is a more apt juxtaposition to the "school of hard knocks". Sure, an MBA and accelerator experience may overlap in many places -- but they sure diverge in many others.
That doesn't stop people from asking the question "Harvard MBA or Y Combinator?" though...
And that's the problem with rankings. Because it matters what you mean by "top tier".
I'd argue that Harvard CS is top tier, it's just much, much smaller than the schools it competes against. Michael Mitzenmacher, Leslie Valiant, Michael Rabin, Greg Morrisett, Eddie Kohler, Krzysztof Gajos, Margo Seltzer, and Barbara Grosz are all among the very best in their fields (or in the case of Grosz, were the very best before they went on to be Dean).
In general the faculty are very, very high quality, but in contrast to a school like MIT or Washington, which have probably 60-80 of faculty, Harvard has only about 30.
I was surprised the article didn't mention this too. It talks a lot about culture, but doesn't really mention that Harvard really isn't the place where people most interested in computer science would want to go, especially at the grad level.
I agree, the "humble" thing about University of Washington was pretty cringe-worthy.