Here's the problem i have with the Mahayana: everyone always thinks their motivation is good.
No, I don't think so. While people can justify their harmful actions in very creative ways, the bottom line is we have all said and done things with the motivation to harm someone or hurt their feelings. We've all done things that we know are motivated by greed or jealousy or pride.
I'm not quite sure what you mean by this being a 'Mahayana problem'? Do you mean you know a Mahayana practitioner who seems to have behaved negatively and claimed they had good motivation? Or that inherently we all think we're always doing the right thing?
It's true that for example, sometimes we feel like we're trying to help someone and, as it turns out, we're not really helping them at all - possibly even causing them harm.
There's 2 important things in play there - 1. it's good (for us) to have a motivation to help others .... 2. the problem is we usually don't have the wisdom to know what's really going to benefit someone else.
That's why practice is so vital - we don't only need the compassion to want to help but we need wisdom (skillful means) to know HOW.
And sometimes, things can look negative (eg 'tough love') but be motivated by compassion and be of benefit.
You'll probably never know someone else's motivation, but what really counts is your own.
Personally I know times when I've had good motivation to be of benefit to someone suffering & hurting others and it's gone totally pear-shaped and ugly - while i'd hoped it had turned out better, I guess I just didn't have the skills and also they didn't want things to change. Still, I'm glad I tried.
As far as our own motivation is concerned, i think it's critical to look deeply into it - you're right, we can fool ourselves that we're doing the right thing, but we have to ask... good for WHO? Are we motivated by our own need for people to do what we want, or what makes us comfortable or fits into our own view or doing 'good' things because it makes us look good/important/holy schmoly/impressive?
Thanks for bringing up an interesting topic!