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A tale of two sources: Is TLS *defense* against Man-in-the-Middle, or not?

We have recently used a security scanning tool to assess security of an application. It raised a particular configuration as a Medium vulnerability. The claims made in the explanation of the discovered vulnerability don't seem to match with industry standards.

The claim is that "transport mode" security is insecure:

"Transport mode is the least secure option and should be avoided."

This quote above comes from this article relating to WCF security:
https://vulncat.hpefod.com/en/detail?id=desc.semantic.dotnet.wcf_misconfiguration_transport_security_enabled#C%23%2fVB.NET%2fASP.NET

The claim here made by HP appears to be that transport layer security, including SSL and TLS, is less secure than message-based security. The article further explicitly states that TLS is susceptible to man-in-the-middle (MITM) attack.

Further research into MITM attacks seems to indicate that the opposite is true: TLS is the preferred way to prevent MITM attack. Resources supporting TLS include:

https://en.wikipedia.org/wiki/Man-in-the-middle_attack

http://stackoverflow.com/questions/549/the-definitive-guide-to-form-based-website-authentication/477578#477578

Do client certificates provide protection against MITM?

So, the question is:
Is there any merit in the claim, by the HP article, that transport-mode security is to be avoided, for the reasons cited in that article?

UPDATE: To add some context- the use case in our situation is calling a webservice, not a public site.