WebGL is a failure in the making. Why? The PC game market is concentrated solely on DirectX and windows. Wait, who owns DirectX ? That's right Microsoft. Oh hold on, what else does Microsoft own, oh it's Silverlight, the flash alternative on windows. Can you not see where this is going ? WebGL aims to be a cross platform 3d solution but Microsoft already owns the entire gaming market, and they are serious about Silverlight, and why in the hell would they give that up? For an open source initiative? Bull**** Given Microsoft's history, this is not their culture. You can forget wetting yourself about WebGL, its not going to happen because a developer will not want to make the same game twice, Microsoft and something called internet explorer(still holds large chunk of market share) is not going to support it. Why? DirectX on Silverlight is coming, to kill Flash even more in this area.
Many people have mentioned Flash the way to go, however, Flash currently seems to have uncertain plans for hardware accelerated 3d in Flash (flash 10 has hardware acceleration but not for 3d). They have failed to take leadership roles in this area and left it to the community, Papervision3d. Papervision3d is great, but nowhere near the performance of hardware accelerated plugins. You can't really play a descent 3d game even with Away3d, as it will lag....The outlook of Flash seems deem when you look at the onslaught of other players, Microsoft and open source movements.
Market penetration is not as important as you think. Clearly, Unity3D is ahead of the competition in 3d web game market. If the game content is good enough, you users will install the unity3d plugin (not like its a spyware of any sort), and enjoy your games.....
As explained earlier, WebGL is a failure in the making, dont bother with it.
Hence, I strongly recommend Unity3D, or wait till something happens in this market.