Based the experiences of others who driven them all over Iraq the HMMWV is as good as it gets.
Are they bomb proof? No, but neither is anything else.
Could they be hardened? Yes, but that adds weights and reduces payload.
Will they burn if blown up? Yes, but so would any other vehicle hit by high explosives.
The one weakness of the HMMWV is the exposure of the gunner on top. Fully exposed from the waist up makes him a prime target for chuckleheads with weapons. Lately, I've seen photos of HMMWV's in Iraq with what looks like improvised gun tubs and shields. This allows the gunner 4 sided protection when firing, reloading or clearing the weapon.
Although, I personally have not read the SOF article I'm wondering why now they would write an article about a vehicle that, in my ever so humble opinion, is a sound vehicle that does what is asked of it and much more.