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Running from the web comes with a huge catch which renders this backup mode useless: PHP meant for web usage has a maximum execution time limit. backup.php requires no time limit, so that it can back up your site.

However, everything is not lost! Akeeba Backup, like its predecessor, comes with the front-end backup mode. In order to enable it you can click on the Configuration toolbar button in Akeeba Backup's control panel page (you have to be a Super Administrator to see this button), enable the front-end backup feature and enter a front-end backup URL. Then, you can follow the same procedure as you would in JoomlaPack. Since Akeeba Backup's documentation is still under construction, you can see JoomlaPack's documentation at http://www.akeebabackup.com/joomlapack-2x/febackups.html.

You haven't enabled the front-end backup feature. First, login as a Super Administrator (just Administrator will NOT do), then go to Akeeba Backup's control panel page. On the upper right hand corner of the page you will find an icon labeled "Parameters". Click on it. A new window pops-up. Set "Enable front-end and remote backup" to "Yes". In the "Secret word" field enter something - keep this somewhere, we'll need it. Click on Save. The window closes.

The URL to run the CRON job is:

http://www.mysite.com/index2.php?option=com_akeeba&view=backup&key=mysecretkey&format=raw 

where "mysecretkey" is what you previously entered in the "Secret Word" field.

Do note that if your host's pseudo-CRON doesn't support redirections, the backup will never complete. In this case, you can't use your host's pseudo-CRON feature to backup your site. The reason is simple: you can't backup your entire site within the strict time limit a single page load must run. This is why Akeeba Backup is 50k lines of code and not about 50-60 lines; most of the code deals with preventing and working around causes of timeouts :D