This sentence is somewhat deceptive in its form, so it's no surprise that folks have difficulty parsing it.
Questions usually create interrogative sentences, but in this case we have an indirect question which actually makes this sentence declarative. Standing on its own (minus its predicate clause and conjunction) the sentence What about Sir Isaac Newton? is a declarative statement the same way I wonder how hot it is today, is. This is our base sentence.
The predicate clause who some contend was autistic following the comma is just adding additional information about our subject Sir Isaac Newton, so this is fine. And that brings us to the first word: but.
Conjunctions like but or and can indeed appear in grammatically valid sentences as the first word. In this case, the word but ties this sentence with the one that comes before it with a meaning of with the exception of.
So, to sum up:
But what about Sir Isaac Newton, who some contend was autistic?
The declarative base is bold italic, with the italic conjunction tying Isaac Newton as an exception to what was described before, and the predicate clause after the comma expounding upon the subject of Sir Isaac Newton.
EDIT (6/30/15)
The question has been brought up by the original poster as to how the sentence "What about Sir Isaac Newton?" is a complete sentence when it lacks a verb. This is a valid question and involves another more complex mechanic of grammar: Ellipsis.
Ellipsis is the omission of one or more words from a clause that are understood in the context of the remaining elements. If the sentence stood alone, the ellipsis would likely be a verb-ellipsis, with the (limited) context pointing toward "what" being used as to inquire the reason or purpose of something.
In your example, however, the entire sentence begins with a conjunction that ties it with the previous sentence. Combined with the understanding of the sentence itself, we can infer that the question inquires after the reason why Sir Isaac Newton is an exception to whatever was listed before. Thus in this case, the verb clause "is different" is what is (most likely) being inferred (pursuant to the content of the previous sentence).