don't forget that the moral of units will make a massive drop when they see a friendly unit rout what can cause a chain rout. Disciplined and elite units will only be affected by another routing unit if the routing unit also is disciplined or elite.

All the countermeasures have been mentioned already: build religious buildings in your troop producing provinces, keep your units flanks protected, keep your general close to endangered points in your line, try to move in a favorable position before committing your troops.

These are of course no hard rules as for every rule there are exceptions or situations where you could/should do something differently. But always be aware of the morale of your troops.