If multiclassing made you exclusively stronger, then yes, a penalty might be worthwhile. But it doesn't. You still GENERALLY get bigger and better class features for sticking with a class. Sure, you might get some short term rewards such as dipping Fighter2 for 2 feats to complete your Tactical feat tree by level 6, but it delays something else that might be cool, like Greater Rage or something. There are plenty of opportunity costs involved with character building, and adding the extra beating that is multiclass penalties is just injury to insult.
Plus, I hate to always bring it back to casters/non-casters, but multiclassing is generally a customization tool for non-casters. All you care about are HP, skill points, and BAB, which ALL classes have in varying degrees. Then its just a matter of duct taping the ones with the features you want together and forming a build. With casters, the only thing that is important is MOAR CASTER LEVELS, in 9/10 cases. Thus, full casting PrCs are generally saught after, which DON'T have multiclass penalties due to their nature as PrCs. Adding levels of Cleric to your Wizard build is a direct nerf in most cases because Cleric levels don't progress Wizard casting. Adding levels of Barbarian (especially Spirit Lion Whirling Frenzy Barbarian) to a Fighter build will make you a better Fighter because it gives you BAB, HP, and skill points, along with whatever other toys are important to you. Adding a Wizard dip, however, is generally less useful because it doesn't give you BAB, it doesn't give you much in the way of HP, and you generally can't utilize much of the spells with your armor and weapons in the way (other than maybe True Strike, but thats not action economic).
Spells are how casters customize. Multiclassing is how non-casters customize. Multiclass penalties only really hurt non-casters.