This is a great question, and there are a few reasons.
First of all, I’ve found the iPad app a bit glitchy. For example, it’s regularly the case that the iPad app will say there are articles unread in a given feed and when I select the feed, there’s nothing there. Similarly, if I mark a feed as read (such as by scrolling, or using the tick mark to mark it all as read) the unread article count also remains.
Sometimes, if I select another feed, and then go back to the feed with the wonky unread count, it will display more articles, and eventually get to 0 and vanish from the list of “feeds with unread content”.
This does not happen on the web interface. It also doesn’t seem to happen on the iOS app.
Secondly, there are instances where new features seem to come out for the web version first, or are web-only. The most important of which for me is the currently superb feature of article clustering. This has been a dream-feature of mine of RSS readers since day nought.
There were probably a few other features where this was the case, and it makes sense, it’s probably easier to update the web-version than update an app and get it pushed out through the various app stores.
I should probably provide better feedback on the iPad glitches I encounter, but the path of least resistance was to simply use the web version, which mostly worked great.