The choice can largely come down to the commercial goals and the purpose of your website. Many businesses who sell products decide to place Adsense adverts within their website. This would appear to be a strange choice, opening up opportunities for rivals to promote their service or product to your potential customer base.
Many publishers claim that they are only doing this to allow companies who provide ancillary services to advertise. These claims have some merit, as those who for example sell pillows could provide those who sell bedding with an opportunity to advertise.