Smithsonian Magazine April 2010

The main points of this article include:

Since the 1930's questions have arisen about his relationship to Alice Liddell.
Since the 1960's his work was tied in to hallucinogenic drugs.
When some photos of his were exhibited in 1999 some considered them of a pedophilic nature.
He made up stories and games for young children (mainly girls.)
He took over 3000 photos. A little over half are of young children.
30 of the photos are of a nude or semi-nude nature. (This makes them 1/100 th of the total photos he took.)
At the time photos such as he took were normal and considered to show the innocence of young children.
The photo of Alice dressed as the beggar girl when she was six was so liked by the family that they kept the photo in a morocco leather-and-velvet case.
Some Victorians considered him a 'child-loving saint.'
In 1933 a professor wrote an article saying that Carroll had a suppressed sexual desire for Alice.
In 1945 one author said Carroll wanted to marry Alice when she got old enough to get married.
There was a split with the Liddell family and one possibility is that the mother (and/or father) objected to his interest in Alice.
There is no evidence to support the idea that he had an 'unhealthy' interest in Alice.
There is a possibility that there was some bad gossip about his interest in Alice/Ina/the governess.
One possibility is that our society has become much more strict about such things as photos of young girls and that English society at the time was not upset about them (they even used some photos on greeting cards.)