Complicated relationship

Ive been separated from my husband for a year now, and we just started working it out. Sad to say that we only started working it out offically after i began to get used to the idea of not being with him. He makes my son and i happy, but there are time where i dont feel loved and very lonely. I plan on spending the rest of my life with him... But theres an overwhelming feeling that i shouldnt be with him. Should i follow my gut and find a future by myself? Or continue with my fragile and lonely marriage with the hopes that it will get better?