You can´t use any Flash/SWF content in iPad, it simply doesn´t work there because Apple´s mobile devices don´t have support for Flash.... any kind of support at all.
You have to convert your animation to html5 and import that format to your iPad magazine by using html/web-view tools which you can probably find from any iPad magazine production tool.
You have couple of options how you can proceed. You can try to use Adobe´s free Wallaby converter from Adobe Labs.
Or another choise is Google´s Swiffy which you can now install as a plugin to your Flash. It converts ActionScript2 timeline animations really nicely to html5.
I have tried with only eDocker Tablet Pubisher´s Add html-content tool and there it worked like a charm. I guess it will work with Adobe DPS`s web-view as well.