I think(?) I've finished up with the rebels, but now I haven't the slightest idea of what to do. Is there a secret journal button that I'm missing?

Also, this game is tough. Any tips?

It's been a long time since I played, but I vaguely recall that once you're done with the rebels (I assume you've been through the various rebel "backup" bases as well?), you need to go to the village and talk to someone to trigger a quest to go explore the Ziggurat on the Eastern end of the island.

As far as tips:
1. Use spells. Attack spells aren't all that useful until you start to get the more powerful ones later in the game, but you should be making regular use of healing and buff spells. Your mana regenerates pretty quickly, so you don't have to be too conservative with it. Also, just in case you didn't notice, you can customize the power of each spell in the spells menu using the blue sliders (though this also affects mana cost).
2. The game world is fairly open, so there are areas you can gain access to early on that will kick your ass. Don't worry about this - it usually just means you need to come back later.
3. Since there's no XP or loot system, dodging past clusters of enemies you don't feel ready to take on is a viable strategy.
4. I don't remember if you've gotten an of the jars of honey yet, but I recommend saving them rather than drinking them right away. Yes, they give you a permanent boost to max HP, but they also instantly refill your health (and possibly mana too, I don't remember), so I tend to save them for use as health potions.

I'm kind of stuck at the Queen Bee boss fight. I really can't understand why this is so insanely hard.

Yeah, I found dodging monsters to be the way to go in general. I also started pumping out the spells, though mana potions are rare which ends up with me sitting around and reading a book (because I love reading books apparently).
I also saw a honey jar in the village, but had no clue how to get it because there's a cloud of bees that instagibs me.

Edit: Thanks for the tips though, I genuinely expected no one to take a look at this game.

I think the trick to that one was to focus on dodging while firing off your spit-projectile whenever you get a moment's breathing space. But again - that's old memories from an old brain here.

EDIT: Alternately, if you have enough health to trade blows with her, you can just park yourself next to her head and chew on it until she dies.

You are correct. Yet, I can't seem to shake the homing projectiles without going into the other room. It's kind of over the top frustrating and I was caught completely off guard by it.

I kind of really wish there was some way to make it easier.

There is a difficulty setting - I don't know if you can change it mid-game, but when you start a new one, when you select that "Larva/maggot/etc" screen you're choosing difficulty level.

I can also recommend playing this game on easier modes, most of the difficulty comes from the camera not working probably, this is especially nasty during boss fights.
The normal monster encounters can and should be simply walked around. Otherwise it comes down to who's got more health/power and buttonsmashing. What sells this game is the exploration, the story and the character of the storyteller. The fights become insanly easy once you get the ranged attack as you can run faster and kill anything at range anyway. Just a matter of time until you've chewed through the hp.