Do children with autism have bigger heads?

Sometimes. Children who go on to develop autism can experience an acceleration in the growth of head circumference around 6 to 12 months of age. Not that their head was large to start with, but that it grows faster than expected. However, the overlap between this and normal head growth is so large that it is not useful information as far as diagnosing a particular person.
In some boys. Several studies have associated regression and enlarged head size in boys with autism. No one fully understands this, though there is increasing evidence that part of normal brain development includes "pruning" of certain areas, especially during puberty and adolescence.