Quran 9:29 does not say "fight in self-defense." It says "fight those who do not believe" in Islam

Quran 9:29:

Fight those who do not believe in Allah, nor in the latter day, nor do they prohibit what Allah and His Messenger [Muhammad] have prohibited, nor follow the religion of truth [Islam], out of those who have been given the Book [the Bible, given to Christian and Jews], until they pay the tax in acknowledgment of [Muslim] superiority and they [Christians and Jews] are in a state of subjection [dhimmitude, i.e., third-class legal status for non-Muslims].
Because Quran Chapter 9, with its verse of the sword (and the above verse, and other supremacist verses), is generally considered by Muslim scholars to be the last or one of the last chapters Muhammad produced, those same scholars often say that it cancels or abrogates the Quran's tolerant chapters and verses, which Muhammad produced early in his career.  Yet the early, more tolerant chapters are still considered valid for Muslims when Muslims are weak and in the minority.  Why?  Because Muhammad was weak and in the minority when he produced those early chapters during the first, Meccan stage of his career.  Orthodox Muslims thus consider the early chapters to be a sacred program valid for the first stages of Islamizing a society.  In later stages of Islamization, when Muslims have become stronger, the Quran's later, supremacist, totalitarian chapters apply and supersede the earlier.

It should be noted when reading the Quran that its chapters are not in chronological order.  Instead, the longer the chapter, the closer it is to the front of the book (generally).  The shorter the chapter, the closer it is to the back of the book.  Thus the sequence in the Quran has nothing to do with when Muhammad produced the chapters.  Naturally that makes the Quran harder to understand.  To read the Quran in chronological order, check out chronquran.blogspot.com.  That site also gives easy access to expert commentary (by Ibn Kathir and Robert Spencer) on each Quran chapter.