Should I choose a research field that I'm not really good at, but have strong interest? I'm a first year masters student. Currently I'm doing coursework but I'll have research in second year. I find all subjects interesting. I feel better when I'm doing subjects including a bit of mathematics and rigorous thinking. Algorithms in particular. 
But I'm not really good at it. I try hard but it's just not happening. Still if I'm given opportunity I want to do research in Algorithms.
This will obviously require mathematical thinking.

Is it good to pursue research career in a subject which I'm interested in ignoring the fact that I do not have strong base and understanding of it? Or should I choose something easier based on my abilities?
Doing research on a subject is the best way to get a good understanding of something.  Presumably, if you do reasonably well in the parts of your coursework covering algorithms (in the eyes of the professors), you're doing well enough.  Mathematics and rigour are hard, even for most people who are capable of doing good work in the area.  Also bear in mind, humans are subject to the impostor syndrome.  If you find a professor who knows you and is willing to guide you in research in this area, then I don't see a problem.