Yeah, if someone is playing an Obviously Monstrous character of the type that's normally kill-on-sight, then they should be kill-on-sight as far as NPC's are concerned until such time as they prove otherwise. You choose to play that race, you are going to have social problems, and that is part of the race. To do otherwise is to do a disservice to the idea of the race and the world you're playing in.
Now, if what you're looking for is the mechanics, and the mechanics aren't overpowered, then maybe you can work with your DM to refluff a normal-looking character into having those mechanics for some reason. But if you're actually looking to play the race, then the social issues are inextricably tied to the race and should never, ever be ignored - that would be a sign of terrible DMing and to expect it is a sign of a player that has no interest in actually roleplaying the character they chose to build.
There are a few places where this isn't true. If you want your players to be able to play monstrous races without harassment, set your campaign somewhere it makes sense. In Sigil, for instance, it doesn't matter what you are, everyone's just going to go 'meh' and treat you pretty much the same - with a little more caution if you're the type that can obviously kill them dead very fast, but there's no mobs with pitchforks to burn the <insert hated race>.
But in more 'typical' settings, don't ever expect to walk into a city if you happen to be a troll. It's pretty much that simple - when the party goes to town, the troll either has a magical disguise or waits outside, hidden in the bushes. The dark elf doesn't openly walk to the gates and demand to be treated equally. Consider that even Drizzt was refused entry to Silverymoon, despite being a personal acquaintance of Alustriel. Only years later after his personal reputation in the area had grown among the common people was he allowed to enter cities in that region of Faerun openly.
