I totally understand this. I have 2 boys, 5 & 7, and I just learned another family wedding will include girl in our family who is 5, and I am sure my kids will not be included. It sounds like your child is well-behaved (or you would have suspected why he was excluded) but it does sounds like if it is your brother's brother-in-law, you could say to your son, "Well, Uncle Groom IS a part of family, but he is what we call 'related by marriage,' and since (explain relation to brother/brother in law) is his closer relative. They see each other more often (or have the same granparents...something like that) and at a wedding, sometimes you can only have SOME people you love, not EVERYBODY you love, so they are only having a few kids, not ALL of the kids they like and love. There isn't room for them all, and wedding usually go after bedtime, so it isn't really a kid's party, it is more like church, and a break, and a fancy dinner party."
Do the bride & groom come to your kid's school plays or birthday parties? Have they ever babysat for you? Are you close enough (in another situation) to leave your child with them for 48 hours? These are ways to talk to your child about what "close, close family" is so he doesn't feel blown off. Your son is cousins with someone who is related to this couple.
You might also tell him that you are not 100% sure you are going, because you don't know if you can find a babysitter that can stay with him for so long, and you might not have fun, because you'd miss him. (Sounds like the truth.) You can also tell him, if you want, that while it looks like a fun party, you really like to go to parties where the whole family is going, because you prefer family fun. (Sounds like that would be true, and you can put some of it on the table without being super gossipy).
When we had our wedding, I was teaching and my students were old enough to drive. They lovingly threatened to crash my weddding (I taught kids with behavioral issues-they were fun and spontaneous). We wrote "adults only reception" on the invite and made a point of making a reference to the cocktail hour time to make it clear that we couldn't accommodate younger kids except the bridal party. I had to really focus on the elegant thing because we couldn't afford the 40% increase in cost if we opened it up to whole families, and there were people for work and from school that I didnt invite because we had to sent a limit somewhere, so having a cousin's kid, and not someone who I saw every day was odd. One family member was very put out, and let me know. We had provided a list of hotels in a few price ranges, and one had a conceirge who could arrange for sitters, if needed. If she had brought her kids, it would have cost me $600 to make it work. They declined the invitation in the end. Another member of this family tried to "show me" by writing in more distant members of their family, to whom nobody spoke, as their "plus one." My mother in law took that on. I don't know what she said but she squashed it, and said something like, "There is a reason that nobody wants her at the party, and you know what it is." (I still don't know what it is). What was strange was that these were people who never called me on the phone to see how I was. Didn't know what I did for a living, didn't know my address but they were mad at me. I told my mom that I didn't feel bad about not inviting people who couldn't pick me out of a police line up.
It sounds like your feelings are really hurt, because this is a pattern of behavior in your family. But this bride and groom didn't start the pattern. They made a choice (which may not be the right choice, but they made it) and it reminds you of all these other choices that happened probably before the couple even met.
I had that too, and it only go better this year. The way I handled the "my brother and my brother's offspring, are treated like gold and my kids get bread crumbs," is by talking to my brother about it. I found out that my brother's "attention" was not what he wanted-he's shy and wondered why he was always thrust into these awkward situations that are hard for him. It was liberating to hear. Not sure why I felt better hearing that he wasn't getting everything he wanted out of his role made me feel better, but it did. I wasn't feeling slighted as he was spoiled. The attention we got just didn't fit either of us. He's asked to take on responsibilities and calls me to say, "I have no freaking idea what to do here." We are better friends, and honestly, that is the one relationship here really worth investing in (not the in laws/2nd generation/aunts & uncles). Plus, your kid, who you respect and love.
As an adult, you don't have to attend. You can send a note (and this is what we do) that says, "I am so happy for you. Unfortunately, we won't be able to attend. Hubby, kid, and I wish you the best. Please send a copy of your wedding photo for our family album." Your family is what it is, and your life right now includes the fact you have a kid who may make it harder for you to participate in some social things. If it is close by, you could also say, "We plan to attend the church service (if it is separate) but wanted to let you know that we won't be able to attend the reception. (The one time we were able to bring a kid to a family wedding, we had to leave early because he got sick, so none of us ate our $300 worth of food. My parents stayed at the wedding instead of offering to take care of my kid at their house, where I was staying, because they didn't want to miss a chance to drive my brother back to the hotel, in case he needed a ride after having a few beers).
We don't take our kids to weddings. That usually means we don't go. We take them to family reunion type parties, but often it is for families we've chosen to make our own, now that we are wiser. You may be headed in that direction. Worth doing some soul-searching about,because how your kid feels about these situations will be based a lot on cues he picks up from you.
Again, though, I am sorry, sincerely, that you keep getting hurt. A good book is "Why Do I Love These People." I bought it for someone in my family, who totally missed the point, but you might get something out of it.
I'm inviting children to my destination wedding in May, mostly because I feel obligated as I'm having my (then) 18 month old nephew come & be the ring bearer. Luckily most of my family members have decided to leave their children at home - with the exception of my 8 year old cousin, who gets everything her little heart desires. 
But, my wedding will be a little more "adult" themed - on a cruise ship, with lots of boozin' and grubbin'. 
So I'm thinking my family members' decision to leave their kids at home is probably more for them and not me, haha.
You do of course realize that the South and midwest actually are part of the real world, don't you? You are painting midwesterners and Southerners with an awfully broad brush there. 
- actually seem to agree that the couple should invite who they want and they don't have to invite kids if they don't want to.
