When it comes to flying and bags, you always have a choice of how to handle them.
Don't want to tip the bellman to bring your bags to or from your room? Carry them yourself. (really, people do this every day)
Don't want to tip a skycap? Don't use them, take your bags to the airline company counter at the airport yourself and check them in there.
Skycap service is for those who are willing to tip a couple bucks to have someone else check them in and handle their bags for them. You can't think of it as paying someone to print a ticket and tag a bag, think of it as paying someone else to take your bags to the airport and checking you in so you don't have to stand in a check in line there. Unfortunately, using ME effectively forces you to use the services of the skycaps (I'm assuming here, since I have never taken ME, but you have to check your bags at the RAC if taking ME, right?)
So, think of it as the price you pay for taking ME and not having to handle your bags at the airport yourself. Remember: nothing's ever really free, LOL!
Now, I have to say as to the OP's situation:
YES, that comment was rude! But I bet they are getting stiffed all the time nowadays since people have just tipped the bellman for bringing their bags to the RAC. That's a sucky set-up, but they should put up a sign or just charge per bag or something, it was rude to say that to you. Disney needs to be more upfront with folks about this ME thing, and make sure they know they will be effectively charged for taking it when they are forced to check bags with skycaps at the RAC.
Lastly, I think you (OP) made a mistake when you tipped TWO bellman (and which is hardly the skycaps fault). When your bags are taken from your room to the front of the hotel, don't tip until the "transaction" was complete. That means: your checked luggage delivered to the RAC, and your carryon's delivered to the holding room. It sounds like folks will need to be sure they specifiy where they want their bags delivered, i.e. "these bags go to RAC, these go to the Bell Services Desk to be held for us". Then, and only then, tip that one person who does that for you. If he walks away before the transaction is complete, no tip. In the end, they pool tips anyway, so no need to tip each bell guy who touches your bags. Tip when the job is complete. Then, tip the skycap, just as you would at the airport. I know it just seems weird to tip two people just because it comes so close together! But really, at the airport, they aren't doing anything more than they are at RAC--you walk up to the skycap desk at the airport and they do the exact same thing as RAC, wouldn't you tip them?
For folks who don't want to tip the skycaps, don't use them. Unfortunately at Disney that sounds like it means not using ME. I guess this is one more reason I like my rental car! Saves me money in skycap tips, LOL! Actually, I have never really understood why people use the skycaps at airports either. It's really the same amount of money to tip a skycap or rent a cart (well, actually depending on how many bags you have, cheaper for a cart), so often we do whichever one looks like it will result in a shorter wait. Although, personally, as someone who has had the airline lose my luggage (permanently!) I like to see my bags go all the way into the system myself, no sense adding levels where things could go wrong!
edited to add, I hope this post doesn't sound harsh, that's not my intention at all, just wanted to point out you always have a choice of using skycaps/bell services--unless taking ME--and pointing out that Disney isn't being totally upfront with people about the "true cost" of taking ME. Sorry in advance if anyone is offended!