Houston looks pretty red to me, although I don't understand why it appears so short in comparison to much smaller cities like Pittsburgh.
I suspect that the height of the counties is based on "net" votes, not total votes.
For example, if Houston had 2 million "red" votes and 1 million "blue" votes, it would be represented by a red column 1 million tall (2 red minus 1 blue), whereas if a city of the same size had 2.7 million "blue" votes and 0.3 million "red" votes, it would be represented by a blue column 2.4 million tall (2.7 minus 0.3).
Not only would that explain the heights seen in the 3D chart, but it would also probably be more informative than a similar chart scaled in a "winner take all" method.
Houston is the 4th largest city in the US. It looks so short because the way they made the map. They made it so that you are looking down on Houston almost vertically. It exaggerates the height of the far northern, far western, and far eastern cities at the expense of the central southern cities (like Houston, Dallas, and New Orleans).
Houston looks pretty red to me, although I don't understand why it appears so short in comparison to much smaller cities like Pittsburgh.