There are several reasons.
Depending on the form of lighting used in a game, antialiasing does not always work. In certain engines, for example, the lighting will ignore AA and re-alias anything near a light source. Developers can sometimes make AA work in deferred lighting engines, but it often ends up dropping performance massively or causing graphical artifacts when it interferes with the game's lighting.
Post AA such as FXAA, MLAA, or SMAA are becoming popular because they work in any engine, with virtually no performance impact, and if implemented properly add only tiny amounts of blur. Most of the dislike I see towards Post AA is coming from people with improperly calibrated monitors, as a sharpen filter or too high of monitor 'sharpness' conflicts with Post AA, reintroduces aliasing and makes Post AA shimmer. This is because monitor sharpness is not real sharpness, but actually another Post Effect that adds edge contrast.
If you want more AA options, Nvidia offers the ability to use compatibility flags to make OGSSAA (ordered grid super sample antialiasing) and SGSSAA (sparse grid super sample antialiasing) work in most games, including ones with deferred lighting engines, though it can take a bit of work to find the right flag.
This is a list I've compiled of Nvidia antialiasing compatibility flags, in games known for lacking rendered antialiasing solutions. There are lists online, but these are mostly values not included in other lists, as I tested them myself. It's important to note that 4x grid supersampling + 4x multisampling still usually just equals 4xSSAA, whereas 2x2SSAA is actually 4xSSAA.
Dishonored
-AA driver bit: 0x000010C1 or 0x200012C1
-AA driver setting: 4xMSAA + 4xSGSSAA
Dark Souls
-AA driver bit: 0x004000C0
-AA driver setting: 4xMSAA (performance) or 2x2SSAA (quality)
Star Wars: The Force Unleashed
-AA driver bit: 0x00000245
-AA driver setting: 4xMSAA + 4xSGSSAA
Zeno Clash 2
-AA driver bit: 0x080000C1
-AA driver setting: 2x2SSAA
Mass Effect
-AA driver bit: 0x080100C5
-AA driver setting: 2x2SSAA
Mass Effect 3
-AA driver bit: 0x000000C1 (default is 0x080100C5)
-AA driver setting: 4xMSAA + 4xSGSSAA
Magicka
-AA driver bit: 0x00012C0
-AA driver setting: 2xMSAA + 2xSGSSAA
Jedi Knight (series)
-AA driver bit: none
-AA driver setting: 4xMSAA+4xSGSSAA
I usually use SMAA or FXAA in games. Their original implementations a few years back were poor, but lately they've been improving, as developers find the benefits of deferred rendering engines too large to ignore. The SMAA injector in particular offers very good quality for Post AA.