First, if your spouse gets a restraining order against your ex, it would not necessarily negatively affect your visitation. It will depend on how the RO is written, and whether you are included as a protected party. But, from what you've described, if your son is supposed to be flying to you to visit then there should not be an issue with the exchange, as you and your ex (and certainly your spouse) do not have to be in the same place. Even if you had to do a hand-off at the airport (depending on how young your child is), you could be there and your spouse could wait at home. If your ex is denying you the visitation rights that you were given in the custody orders, I would suggest that you contact her (email if you can so there is a written record) and ask her civilly for him to come and visit you. Be flexible - give several suggested times and tell her that if none of those work, for her to suggest a time and that you will accommodate her. If she doesn't respond, then you need to file a motion to enforce the custody order. Good luck.
Please note that this answer does not constitute legal advice, and should not be relied on, as each situation is fact specific, and it is not possible to evaluate a legal problem without a comprehensive consultation and review of all the facts and court pleadings filed in the case. This answer does not create an attorney-client relationship.