When we look at a standing human being's legs, they look straight.

However, if we could see the person's skeleton, we would notice his or her femurs (thigh bones) angle inward, sort of what we call "knock-kneed."

Furthermore, when we stand, we stand with our feet side by side, a little more than a foot apart, but closer together than our shoulders.

As we walk, our footprints get closer together than we stand.

The faster we walk, the closer together our footprints get, until, at a run, our footprints fall on the same line.

Just bookmark that thought.

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We have a very high percentage of elite bicyclists in my community.

When they pass me, as they often do, I notice the straightness of their legs, and how one line goes up from their pedals, through their ankles and their knees to their hips.

That said, a significant number of us non-elite, normal bicyclists ride with our knees and thighs almost brushing the top tube.

I formerly did that, and thought it a good cure for my knee issues (it worked for me).

Recently, my knee specialist, who does the knees of the US Ski Team, prescribed a bicycle fitting for me with one of the world's foremost bicycle fitters.
This bicycle fitter has such a good reputation in the medical community and amongst elite bicyclists (he has fitted at least one Tour de France winner), that my regular Physical Therapist (who lectures nationally) offered to pay for half of my fitting if he could sit in on the fitting and learn.
One of my co-workers, who holds the record for the Australian Ironman, and whose son (I think) won the American Junior Criterium last year (rides a fixie and trains with the US Olympic bicycle team), uses the same bike fitter.

So, they have all noted this accommodation of mine, in which I almost brush the top tube; and they have described it as a very healthy solution to my body mechanics issues, and a common one.
Nonetheless, this bike fitter and my physical therapist spent two hours adjusting my cleats and making foot orthotics for me, in order to straighten out my legs.
Working in front of a mirror, with lasers shining a line up my legs, they got my legs perfectly straight.
Still, I notice after two weeks that I have started to bend my knees in just a little, as I did before, but no where near as much.
I mean, my legs probably look straight to the casual observer, but not to me.

What if I hadn't had this fitting?
Would it hurt my legs or knees to continue to brush the top tube?
No.
Just the opposite.

Remember above when I described how our human knees incline towards each other, and our feet get on line the faster we go?
Well, for many of us, our knees and feet want to do that on a bike, and the more so the faster we spin.
For many people, knees and thighs inward toward the top tube represents a good knee accommodation, especially so since our pedals (and the bike frame between our feet) keep our feet from getting on line with each other.