At the request of a friend, here are the reasons I boycott Chapters/Indigo:
1. Chapters’ business strategy when they open a new outlet is to reduce prices on everything at that store to ridiculously low prices. They can do this because they are a huge chain. People think “why would I pay more at the independent place across the street?” and thus begin spending their money at Chapters. When the independent place across the street goes out of business 3-6 months later, the ridiculously low prices conveniently go back up. They have a similar strategy with staff. They overstaff during the opening months so that there is always someone to help you. Good luck a year later.
2. Because Chapters has immense buying power, they can bully publishers and distributors. They make demands – returns policies, etc – that no other bookseller would dare to do, and the distributors vying for the Chapters contract buckle. The simplest example of this is exerting pressure to lower prices, making it harder for smaller publishers to stay in business.
2b. I worked in the Raincoast Distribution warehouse for a year or two, and we had a basic stickering policy (for example – if the book has a US price tag on it but doesn’t specify that the book is in US, we put a sticker with the correct Canadian price on it). The stickering policy for Chapters is too boring to go into (and my memory is a little dull) but it was way more involved and Draconian and everyone at the warehouse hated it.
2c. They would also order 50,000 books one week and then return 30,000 of them the next – with the distributor paying the expense.
3. Straight from wikipedia: After the Indigo takeover, Chapters has on several occasions refused to stock certain books and magazines for their controversial content. These include Adolf Hitler’s Mein Kampf , several titles by David Icke, as well as Firearm magazines  and an issue of Harper’s Magazine
4. Heather Reisman, the President and Chief Executive Officer of Indigo, supports the Conservative Party and Stephen Harper – who as we know opposes abortion, same-sex marriage and the Kyoto Accord, and is a member of an evangelical Church that promotes missionary work.
5. In a general sense, I believe that it is in one’s best interest to buy locally. If I buy an art book from RX Comics or Oscar’s Books or Pulp Fiction, the people who own the store and work there will get the money. Now maybe – just maybe – one of those people will come to a show by The Darkest of the Hillside Thickets and buy a CD from me. Or maybe if I have an art show or publish a comic book they will be more likely to display it there, because they know me as a regular customer or maybe they have a similar ethic of supporting the local community. If my book-buying money is going to Toronto, that expenditure has a much smaller chance of being useful to me in any reciprocal way.