I have never liked nor seen the point of using URL shortening services such as bit.ly, is.gd . The only time I have used it is during lectures or talks when links are shared by copying them directly off the whiteboard or slides. Even then, there are probably better ways to share the links such through QR codes or even putting the links on a temporary website or google document that is open for everyone to access.
Yes, twitter's 140 character limit might warrant the need for URL shortening but twitter already has its own t.co shortener. These standalone services only add additional errors or complications. For example, certain scam or phishing sites might have gone under the radar and by cloaking the URL, unsuspecting users might be compromised. On the other end of the spectrum, false positives might be triggered and the owner of a legitimate site might suffer huge reputation damage due to the service flagging his site as a potentially dangerous one. This problem seems to be quite widespread with numerous posts about it. In addition, shortening an already shortened URL (unintentionally or otherwise) is also likely to trigger such a warning.
Most browsers such as Firefox and Chrome do have inbuilt mechanisms to flag out suspicious sites. Search Engines like google do also warn if a site is suspected to contain malicious content. I believe there is no need for yet another layer for checking, especially if it is not done properly.