The Source engine was developed in the early days of DX9 and programmable shaders. At this time, OpenGL had no standardized shader support whatsoever (and OpenGL never got standardized support for SM1.x hardware at all, while this was one of the primary hardware targets of HL2). It simply wasn't possible to write a game like Half Life 2 with OpenGL at that time, unless you wanted to include a separate render path for all hardware out there. Doom 3 tried, and failed. Apart from being more than a year late, the hardware compatibility left a lot to be desired, and Doom 3 only ran properly on a small selection of midrange-to-high-end Radeons and GeForces, where Half Life 2 was very scalable and even ran on DX7-class IGPs.
The Source engine is still used today on a variety of DX9+ hardware, while Doom 3 is nothing but a bad memory (and Rage didn't improve much on that... again late, poor hardware support, generally not a very decent game technically).
Today the situation is quite different: DX11 is nearly 3 years old, and OpenGL has more or less caught up. AMD, nVidia and Intel all have OpenGL 4.0+ support now, and shaders have been covered quite well with GLSL.