Madison's a great place to commute. There's an extensive network of bike paths along with fairly wide bike lanes. It's so easy to get around by bike that I park my car Sunday night and don't have to use it again until I leave town or do massive grocery shopping.
I've also lived in Houston, and I have to agree with the op that it's hit and miss. The trails and lanes that do exist in Houston are decent, but the amount of the city you can cover by using them is limited. The bayou trails, for example, are nice for an afternoon ride, especially if you don't mind looping it, but they don't really take you anywhere. . .Plus, there's a militantly car-centric attitude that pervades Houston's roads, which makes for some pretty hair-raising commutes. It's so darn hot down there that drivers assume that you would be driving something with a/c if you could afford to, and so cyclist = poor + worthy of derision, even if you're rolling on a couple Gs worth of bike. The cat calls and taunts are mostly hilarious, even though it's pretty intimidating to realize that a crazy guy in a pickup is on your tail.