I know this is just a single study with a very small sample size, but it should help shed a scientific light on the topic.
http://digitalcommons.ilr.cornell.edu/cgi/viewcontent.cgi?article=1020&context=institutesIn this study, Cornell University set up a matched-pair test to see if high-end retail stores in New York City would discriminate against an applicant just because he/she was transgender. They sent out two identically-experienced resumes for each matched pair, also matching the pair by age and race and education, with the only difference being that one applicant was transgender while the other one was cis. They used 2 matched pairs, one MtF/cis-female and one FtM/cis-male.
The cis controls received a total of 14 job offers. The trans applicants received only 2. Both of which were from the FtM applicant. The MtF applicant received absolutely zero.
This study shows that all trans people are the target of quite significant discrimination. MtFs might have it a little worse, but really both are horrible and completely unacceptable.