Yeah, but who wouldn't? He couldn't see him, and got the drop on him. He was forced to enter to save Raiden's ass.
As we saw Raiden take out Vamp in direct combat, it's safe to say Snake could as well. (Not saying you're saying he couldn't however)
Remember that it's not only the people they face that equals how good they are. I've yet to see Big Boss jump over missiles, dodge bullets that have already been fired (meaning he dodges in over the speed of sound to get away), as well as jumping several meters up in the air.
Big Boss is good, but I doubt he compares to that. Besides, Gray Fox as how he was in MGS one as a cyborg ninja rapes Null, and Big Boss barley defeated Null. It was even stated he couldn't take him in direct combat but needed to utilize his experience and the terrain.