I sometimes DM and sometimes play, so I come in on both sides of this arguement, since I know I have, at times, questioned DM calls. For better or worse, I am the guy with the best knowledge of rules in the group. Don't get me wrong, if I get hit for 80% of my hps in a single blow, I can live (well, sometimes I
can't) with it. DM calls I question are ones that seem to run totally contrary to the rules without an established house rule to justify the change. For example:
My cleric walks into a room with some undead in it and a big baddie on the far side. He turns undead and plans to walk across to face the "boss." My DM said the turning doesn't work--no dice, no turn check.
In his defense, the reason he did this is because we're in the middle of an undead-heavy portion of the campaign and he didn't want my character to dominate play (But, I feel in moments like this it gives the cleric a chance to shine, just like Barbarians shine in dealing damage, Bards shine in social settings, etc.). But, imho, there are tons of ways to better accomplish the goal. 1. Give 'em turn resistance +4 or something. My cleric is only 3rd level, so it's not like he can overpower that with any degree of reliability. 2. Give us some living henchmen to fight. 3. Set the fight in an unhallowed temple. 4. Make them bigger undead--God knows we need the xp. I picked cleric as my class in part because of the turn undead ability.

I can't stand it when player abilities are taken away spur of the moment for no mechanical reason (and with alternatives that would still allow for storyline advancement).
On another, less important moment, he had an Ettin using a longspear "choked" so he could hit us in adjacent squares. (Which was quite a surprise once we determined our strategy). If the same option was open to
enlarged players or something (as house rule or homebrew feat), it would be cool, but it's not. Weapons and spells should work exactly the same for players as they do for NPCs, otherwise the DM runs the risk of creating "uber" weapons/spells and ends up making the game DM vs. Player, which isn't fun for anyone.
Some of the earlier examples cited, I would side with the DM.
Why is he trying to sunder our weapons?
Because he took the feat.
Why did the golem lose its balance?
A combination of strength of current and silt on the bottom of the riverbed.
Why did the charging giant power attack?
When do giants not power attack?
All-in-all, it comes down to presentation. If you can talk with your DM (or players) about why you think a ruling was wrong or unfair in a civil way, your group will be much happier for it. Sometimes that's in-session and sometimes that's after the game, ymmv.