700c wheels have a longer circumference than 650c wheels. So, if you pedal at the exact same cadence and use the same exact gear ratio, and all other factors being equal, when you use 700c wheels you will cover a longer distance for each revolution than you would cover with 650c.
Yes, you are right. If you are in a 53x16 gear using a 700c wheel, pedaling at the same revolutions per minute, you will indeed be going a bit faster and covering a bit more ground than if you were riding that gear with a smaller diameter (e.g., 650c) wheel. However, if you are that same strong rider wanting to go the same speed using a slightly smaller diameter wheel (like 650c), you can simply just shift up a gear, say a 53x14, and you will be able to attain the same speed.

If you want to calculate gear inches, e.g., how far you are traveling per revolution of the wheel, you take the number of the teeth of the rear cog (say 13) and divide it into the number of teeth of your front chainring (say 52 teeth) and multiply it by the inch diameter of the wheel. I don't have my little metric conversion chart handy at home on a Sunday evening, but the point is, you can achieve the same speed regardless of wheel size by simply choosing a slightly bigger gear.

So, for a smaller wheeled bike, your largest gear, assuming you have the same drivetrain set up as you would on a 700c wheeld bike, will indeed be a bit smaller. If you are regularly spinning out on your 53 x 11 gear (ha ha) then, yes, your smaller wheels are "interfering with your speed." But for such phenoms/freaks of nature, this can be remedied by putting a larger gear on your bike, whether it is a bigger chainring or smaller rear cog.

If we were regularly spinning out our 53 x 11 gears on our 650c wheeled bikes, I would say, yes, the wheel diameter is affecting our speed (or, just as true, our gear choice/set up is affecting our speed). But I don't believe I have ever found a racer or all-around rider who ever is spinning out their biggest gear unless they are in an insane, suicidal mood descending a plus 10 degree descent and going for some speed record.

It just isn't an issue in real-world cycling.

Seriously: How often are you spinning out your biggest gear?

Does this make sense?

The argument for wheel resistance being higher for a smaller wheel has to do with the amount of wheel contacting the ground, the "tire patch" that makes contact with the road. It is a miniscule (MINISCULE) amount less for a smaller diameter wheel. Over really long distances this will translate into a tiny, tiny difference, speed-wise. But for 99.7 percent of us, with the riding we like to do, even at a very high level, even if we are very fit, we will never notice the difference. And, for the smaller folks, if our frame fits us better--as it is not being compromised by being stretched and contorted around giant wheels--the fact that we can attain a more efficient and balanced position with the geometries possible using a smaller wheel, this will make us much faster, and that miniscule speed difference will be beyond negligible given the benefits of achieving a better fit and weight distribution over both wheels.