AnnieBrooke is right. Your husband should keep his little comments to himself... if there is anything I despise, it is an insensitive step parent!
somethings def going on you should talk to him and get to the bottom of it
If the new man in your life were the child's father and his son came in and said he had bad dreams and wanted to snuggle up for reassurance, his father would say "Sure, come on." Your new husband is being kind of a jerk to label this as psychological problems and to tell you to 'make a man' of your son. It's clear that he (your son) is not doing this for kinky reasons, he is going through a period of anxiety and is (logically enough) turning to you for reassurance that everything is still all right.
Talk with a child's counselor with your husband sitting right there and go over it and set up a plan. Try not to kick your son out of the comfort of your presence right at the same time as you have added a new person to the family who gets to be in your presence whenever he feels like it.
Have you talked to him about this, and asked what is scaring him? What kind of bad dreams he's having? I don't think it's a big deal since it's not that often and he appears to be okay in every other way. Ask him what you can do to make things less scary for him, like leave a light on etc. He may be feeling a little insecure with the new man in your life, and reassurance may help. I wouldn't make a big deal of it, but I would make sure you have a line of communication going with him so that you know what his feelings are. and help him deal with them. God luck and take care.
At 12 years old, he certainly shouldn't be in your bed. There must be something else going on that's bothering him and you need to get down to the bottom of that. As far as "making a man out of him", that's an insensitive comment on your husband's part. Maybe try talking to your pediatrician about the situation so he/she can point you in the right direction. He SHOULD feel safe coming to you, but shouldn't be allowed to share your bed, ESPECIALLY as a newlywed.