I've actually been a card carrying member of both (although not both in the airline industry) and am now a member of ALPA. That's just background and has very little to do with what I'm about to say.
In general, the IBT has very tightly knit local unions (the ones that are actually on each property) and a less well knit national (maybe international for all I know) union. In other words, when a pilot group organizes around the IBT they, locally, tend to have some amount of power, and that often results in good contracts such as Republic and Horizon. On a side note, I have no idea how good Horizon's contract is or isn't with out the CRJ rates as part of it.
On an ALPA property, some local unions are very strong (generally the bigger ones) and some aren't. However, the National level of the Union tends to be much more tightly knit. Now, I'm saying everybody gets along, I'm just saying that there is a lot more information flow and resources available to the individual pilot groups.
Many people complain about the 1.96% (and it probably is going to be more in a year or so) that they have to give up for "nothing in return". You actually get a fair amount back from your 1.96%
I just got back from 4 days of Negotiating Training put on by ALPA National. It was actually very interesting, and I learned a whole lot. The level of expertise of the various speakers and trainers that I came in contact with was pretty amazing. Were talking about the people that literally wrote, or designed many of the labor laws we work under today.
And that's just Negotiating. They hold many other training events and conferences. The training and expertise they provide allows members to represent other members in all facets of airline operation. They protect that from discipline. They represent them during negotiations. They help them when they have aeromedical questions. They provide consoling during family crisis or drug/alcohol problems. And the member pilots learn how to do all these things and are supported while doing them by a huge professional staff at National.
Does the IBT have that? I have no idea. I know for the short time I carried an card I was never exposed to any of that.
And that's just stuff that pertains to the individual pilot groups. On a larger scale, ALPA facilitates pattern bargaining which, in theory, allows all other carriers to benefit when it is their turn to go to the table. The provide a way for multiple pilot groups to get together and work through issues that face their part of the industry (think fee for departure, think freight, think polar routes etc) and, in theory, maybe in the future, will allow some sort of career protections at another carrier, should yours go away.
Is it all rainbows and butterflies? No, certainly not. At dinner last night (which, by the way, despite many members who think otherwise was not a lavish prime rib dinner... it was tasty, but not the huge expensive spread some people seem to think exists), the President of ALPA was answering some questions. They were talking about how, despite the Delta MEC originally signing a deal directly with their management right after the NWA merger was announced (which ticked off many NWA pilots), down the road that deal will result in up to 15% pay raises for both groups.
So one of the guys at my table (who works for the same regional I do) raised his hand and said (and I'm paraphrasing) "well, that's nice that the "named" carriers (I guess that's what we are calling the guys who don't have "express" written after the name) are going to make a bunch back, but what about all the DCI and Airlink guys who are going to face consolidation and the likely loss of jobs because of this. Where's their 15%". And the President of ALPA completly danced around the issue (or didn't understand it) and never answered the question.
So, as I said, are their downsides to ALPA? Certainly. In my opinion do the upsides WAY outweigh the downsides? No question at all.
And just one other note...
You asked a fairly contentious (at least to some people) question. Hence, the contentious answers. People feel pretty strongly about some of this stuff. Keep in mind, most of the answers that come back like that are from people are are on the very outer edge of either pro or anti ALPA/IBT/Union/Anti-Union/whatever ism. Why they are there is a question that you have to ask yourself to make some sense of their response. It could be do to any number of things, which I won't speculate about because I'm damn sure I'd offend various people if I did.
Keep in mind though, there are many people on this board who have next to no experience with some things. That's not just the case in this subject but in many different posts this happens. Think the Flight Simmer who is arguing with the 747 captain about how the best way to land the real plane is. That doesn't mean their opinion is wrong. The mark of a true professional is ask these people to expound on their views so you can better understand where they are coming from and why they are saying what they are. It's often difficult to do that in a text only environment.
If you are in fact at Colgan, I would hope you guys end up with a Union this time around (and not a joke like the CPG). And I would hope it is ALPA because that would protect not only you, but also the pilots at 9E, as well as all other ALPA groups (and non ALPA groups) that may fly the Q400 in the future.