This setting is checked by default. This is because the Canonical URLs setting protects you from being punished by Google for duplicate content, or having multiple URLs leading to the same content. Google has a post on their Webmaster Central Blog which details the issues Googlebot faces with indexing duplicate content and how to avoid it. Remember, having this box checked helps you follow Google’s rules.
For more information, refer to this post by Google.
No Pagination for Canonical URLs
This option was added for those users who want to remove the pagination from Canonical URLs. Typically the Canonical URL for a paginated page or post will be displayed at http://mydomain.com/page/2/. This option removes the /page/2/ from the Canonical URL.
Enable Custom Canonical URLs
Use Original Title
User Schema.org Markup
This option was added for those users who do not want All in One SEO Pack outputting any Schema.org markup on their site. We are gradually adding more support throughout the plugin for Schema.org markup because this markup is what provides search engines with the information so that they can display rich snippets. However, the W3C HTML Validation Tool does not support this new markup and will return errors when it sees this markup on a site. These errors can safely be ignored, they don’t affect the operation of a site or the SEO or ranking on search engines. However, for those who prefer clean HTML markup that passes the W3C Validator and are willing to sacrifice rich snippets in search results, this option will remove any Schema.org markup output by All in One SEO Pack. This option is checked by default because for SEO purposes Schema.org markup is good.
You can find out more about rich snippets on Google’s site at https://support.google.com/webmasters/answer/99170?hl=en.
Log Important Events
The Log Important Events option generates a log file of events occurring within the All in One SEO Pack plugin. This is mainly used for debugging and reporting and can be safely left unchecked unless instructed to check it by our Support Team in our Premium Support Forums.