Should the input to the negative log likelihood loss function be probabilities? I am trying to train a supervised model where the output from the model is output of a linear function $WX + b$. Kindly note that I'm not using any softmax or $\log$ softmax on the result of the linear. I am using negative log-likelihood loss function, which takes the input as the linear output from the model and the true labels. I am getting decent accuracy by doing this, but I have read that the input to negative log-likelihood function must be probabilities. Am I doing something wrong?
This seems pretty reasonable to me. You can optimize for any function that is proportionate to the negative log-likelihood. Conventionally, we assume that the likelihood of piece of data under a linear model is proportionate to some sort of gaussian function of the difference between the predicted value and the observed value. If you're a Bayesian you'd say this is a probability. If you're a hardcore frequentist, you might quibble about that, but it's still a number between 0 and 1.

If you take the log of this likelihood function however, you'll get a quadratic function of the difference, with some scalers that you don't need to worry about. So you ought to minimize:

$$\sum_y (y-\hat{y})^2$$

This is not a probability, but since it is proportionate to the log of the original likelihood function (which was, in some sense), minimizing it will also minimize the original function.

Hope that helps!