I don't have a problem to accept the relative strong army of Czechoslovakia in 1938 depicted in this thread or their will to fight.
Still I have to wonder how Germany could take the rest of it just like that in March 1939. Were they simply too surprised? Did they hope for another compromise? I don't get it.
Masada explained it partially, but the plan was to fight on the borders and delay the Wehrmacht as long as possible to give Western allies time to strike against the exposed Western frontier. The plan was a folly since the French has absolutely no will to do that, but they of course kept the Czechs ensured that they'd come to their aid (they lied, yes). Czechoslovakia had even built large and well-equipped modern airbases which were meant to host Allied fighters once the war would begin.
If Wehrmacht wasn't stopped in the border regions (Sudeten Germans would suffer heavily due to the fighting), the plan was to gradually withdraw to the 2nd and 3rd line of fortifications deeper in the interior, while maintaining strong rear guard action and flexible defense. Eventually if everything failed, the Czechoslovak forces would withdraw to Slovakia and maintain its resistance in the difficult terrain until the West defeats Germany.
Now you can see why Czechoslovakia in 1939 couldn't hope to resist. I's fortification lines were gone, its morale crushed, Slovakia was increasingly rebellious and the Western Allies had betrayed it. It was believed that if the Czech president refused to cave to Hitler's pressure, the Luftwaffe would launch terror raids against Czech cities and massacre tens of thousands of people.
And since the Czechs are not Poles who always go into hopeless battles to get killed, we accepted the inevitable. The pro-democratic minded politicians were already in exile, literally hoping for a big war so that they could maintain hope for some sort of liberation.
The Czechoslovakian armies plans were predicated on a defensive war operating from a very strong defensive positions. They lost that and consequently were caught majorly out of position with an army that had no defensive terrain to even the odds. Strategically it was all in Germany's favor - a quick clear shot across relatively flat terrain with excellent roads. It also doesn't help that Czechoslovakia lost its industrial heartlands.
It lost a good part of its industry, but not the "heartlands". Sudeten German regions were mostly rural with only few bigger cities and important industries.
Much more crippling was the severing of important railroads which made life very difficult economically for the rump Czechoslovakia.