While it is critically viable to say there are two protagonists, I don't see the viability is suggesting that Mrs. Jones is not classed as a protagonist. Protagonist may substitute the word hero, and Mrs. Jones is certainly heroic in character and actions: she sees a crushing problem oppressing what might rightly be described as a hapless victim of fate (socio-economic limitations, restrictions, and prejudice) and delivers him by giving him a new view of and opportunity in life. Hughes certainly casts her as a hero of the ordinary humanity sort that echoes the Romanticism of Wordsworth: she recognizes the humanity of the boy who makes "contact with" her; she attends to and relieves the boy's needs; she recognizes the boy's individuality and dignity; she teaches right from wrong; she bestows forgiveness; she ushers in a new opportunity.

While Roger might not have the characteristics of a hardened antagonist, he violates Mrs. Jones peace, attempts to rob her, commits social and legal wrong. Since we and Mrs.Jones and Hughes have sympathy for and connection with and hope for Roger, it might be best to cast Roger as a second protagonist and caste society as the antagonist, as it is clear from the text and Hughes' tone that Mrs. Jones is the hero, the guiding light, the protagonist of "Thank You, M'am," an analysis even confirmed in the title, which, though spoken by Roger, highlights Mrs. Jones.

I must admit, my first feeeling is that Mrs. Jones is the protagonist of this story. She is the one after all who is stopped by Roger and then tries to "convert" him and give him a moral lesson that will have far-reaching consequences on Roger's life. However, I do think this is a matter of opinion and definitely not a clear cut issue.

In one sense the protagonist is Roger and the antagonist is Mrs. Jones.  She, after all, is the one who creates obstacles for him in a variety of ways.

On the other hand, she might be considered the protagonist in the sense that she is the central character -- the one who is most active and who takes most control of the story's plot.

For a good brief critical discussion of the story, please follow this link:

http://www.enotes.com/thank-you-mam-salem/thank-you-mam

I think that you can go a couple of ways here.  I think the best protagonist is Roger.  The reason for that is that he has a clear antagonist.  His antagonist is himself.  He has to fight against his own conscience.  I think that that is the main conflict going on in the story -- it's between Roger and himself.