this discrimination is a mix of factors of past and present.
most of the muslims who have adopted islam in india were from communities who were doing manual labour in earlier days.
and then, after independence also, their education level has not improved vastly.
compare this with education of some smaller,more cloely knit communities like ismailis, daudi voras, jafri momins etc. they have done much better compared to other muslims.
unless muslims try to improve their education levels, they will feel discriminated (and congress enjoys it).
hindus in gujarat feel that congress is favouring muslims, but peronally i feel that congress has done nothing form muslims except using them as vote banks and keeping them backward.