That's easy.

1)Above ground is cheaper.

2) They thought they could get away with it.

3)They knew that below-ground construction would have easily given it away to satellite reconnaissance as a high-value clandestine facility, and it would still be vulnerable to air attack anyway. A subterranean factory may be hard to spot when completed, but the construction phase takes a long time and sticks out like a sore thumb! Building it in plain view gave them at least a chance it might be overlooked or mistaken for something else.

I believe that Israel had some justification in attacking a facility that potentially was a grave threat to its security. But try to look at it from the Syrian's point of view, too. Using that same logic, wouldn't they also have been justified in launching a a pre-emptive strike on the facilities Israel used to assemble its alleged nuclear devices? After all, Israel was building a nuclear capability way before any of her neighbors or enemies were even close to one. That might just be considered by some to be a provocative, if not aggressive, act. And how would we have reacted to such a Syrian strike on Israel? Would we not have mobilized in a heartbeat to protect our ally? And would not our enemies mobilize to protect theirs? If nuclear shit hits the fan in the middle east, who is right and who is wrong will simply not matter.

The Book of Revelations might be right after all. If the end comes, it may very well start here.