Reading the articles by Phil Plait, I have to think that he's gone a little too far - he's vociferously anti-Jenny, and it comes out as a bias.
Going through some of the science and research on this subject from both sides, I think there is legitimate reason to question big pharma on the safety of vaccines, especially when they have been shielded from lawsuits which makes them far less likely to be concerned about the products they're pushing.
For those who don't have children, you probably don't know but the current schedule recommends vaccines for more than three times the number of diseases as most people of child-bearing age had when they were kids. 34 doses total, 24 of which are in the first year. And most are given through in an aggressive schedule with multiple injections per visit. The infant body does react to these injections, sometimes severely. Autism, no. But injury and death, yes. And if that's the case (which is verified) then why subject children to so many shots in such a short period of time? Wouldn't scientific methodology suggest that each dose be given individually so that if the child has a reaction, it can be linked to the source, and so that a child doesn't have compound reactions to multiple vaccines?
Don't get me wrong - I think vaccines are very important and have done a lot of good. And I'm no fan of Jenny McCarthy. But people who point out dangers and suggest alternative schedules do have legitimate concerns.