I too think this is one that you need to look into and read about yourself - people have very fixed ideas about this subject.
I'm of the opinion that there is quite a lot of very solid evidence which shows that there is a subgroup of susceptible children who react badly to MMR. The problem is knowing if your child is in this group or not. For political reasons we currently have no screening process for this but the histories of children who regressed following MMR point to a history of autoimmune disease or mitochondrial disorder as being risk factors. A history of heavy antibiotic use, repeated ear infections and food allergies also appear indicative. Boys are more at risk than girls
As you say the original study which first raised the issue of MMR and autism was based on 12 children. This paper was published 12 years ago and since then a lot more research has been done and hundreds if not thousands of children have been examined now. For example there are currently 5000 cases waiting to be ruled in the Omnibus Proceedings in the US. The findings in the original paper have been replicated and built on.
Musukebba is correct that the MMR does not contain mercury as it is a live vaccine. The suspected problem with MMR is partly to do with the fact that it is given later on in a fairly heavy vaccine schedule following vaccines which do contain mercury and which may (in susceptible children) have synergistic and cumulative effect. Plus the fact that the MMR itself poses a different challenge to the immune system in terms of an atypical exposure compared to single vaccines (or natural exposure).
Musukebba also says this;
"Theories that getting all three attenuated viruses in one vaccine are too much for an infant's immune system are baseless nonsense."
This opinion could be contested based on the fact that the MMRV vaccine which contains MMR plus chicken pox has a much higher level of adverse reaction than the MMR alone. Indeed this vaccine had to be withdrawn in the US because it was unsafe. Additionally there is evidence that the amount of virus in the mumps part of the MMR had to be increased (in relation to the single vaccine) in order stimulate an adequate immune response due to the measles and mumps viruses interacting. This clearly shows that the number of viruses in a vaccine being of concern is not based on nonsense.
It has also been shown that when populations contract wild measles and another (wild) virus such as mumps in a close temporal association, the risk for adverse event and bowel disease (Chron's disease, IBS, ulcerative colitis) increases.
I think this is a very complicated issue that unfortunately it is difficult to get clear information on and to discuss in a non polarised way.
You ask why MMR is supposed to be related by autism - I have watched a very interesting video of Dr Wakefield presenting the theory and the science upon which it is based at a conference. I can post a link to it if you want. Don't want to force it on you as this is an emotive subject (and the video is an hour long!).
Leaving the actual vaccine itself to one side for a moment, there are plenty of people who prefer to give singles because they want to select the vaccines their children are given. Personally as mother to two girls I much prefer to give my children the opportunity to contract rubella naturally so that they will be more likely to be protected into adulthood. The MMR is having the unfortunate side effect of pushing these diseases into older age groups - this is a concern with both mumps and rubella. (The same problem is being seen in the US with chicken pox.)