One possible reason is that there is the concern that a BT does not know how to run a religious home. BT’s may be committed now, as an adult, but they never grew up in a frum community. Therefore they don’t know a frum way to raise their children (besides reading about it or occasionally seeing it). The same reasoning may apply to other parts of Jewish life.
I think that some frum people think that since they don’t live an immoral, hedonistic life because of the Torah, that others – who don’t follow the Torah – must have done all that. People may reject someone whom they fear as being previously a substance abuser, immoral, etc… The fear may not be rational, but it’s there.