When you say your father isn't very understanding about religious differences, is he not understanding in more of a "has a temper tantrum, makes unreasonable demands, sulks, and eventually gets over it" sort of way, or a "throws you out of the house and disowns you" sort of way? If it's the former, then both of you will have an opportunity to grow and better understand each other if you're candid with him about your religious beliefs. If it's the latter, then you are probably better off keeping your beliefs to yourself until you can support yourself.
I think that
ERHR and the other posters who have suggested that you have an adult discussion with your father about your beliefs make a really good point. It wouldn't necessarily need to be confrontational (i.e., focus on how much you love him and respect him and how much whatever path you're on means to you, NOT on how much you don't want to go to church with them). If you know (or can learn beforehand) how to avoid getting drawn into an argument with him, it would probably help you in the long run. It might help to have a series of small, informal discussions (with the church attendance one coming towards the end).
If you really can't talk to your dad about religion (which would be unfortunate, IMO), then your options are kind of limited. Moving out would probably be good for a number of reasons, but if it's not feasible then it's not feasible. You could also go out of respect (or guilt, as I think you stated) and be unhappy about having to do it. But you do have other options.
If you do decide to go to church with them, can you make it into a more worthwhile spiritual experience for you? (You don't say what your own beliefs or theirs are, but are there any elements of their church's doctrines and services that reaffirm or explore aspects of your own beliefs? If respecting your parents is a religious thing for you, could you make church attendance about that? Does the music move you at all? Do you experience any sense of fellowship?)
Seeing as you're not getting much out of it spiritually anyway, would it really be bad to focus on the social or ephemeral aspects of the services that you do like, regardless of whether or not it's something that you "should" be attending church to experience?
Is your place of employment open on Sunday mornings? Could you reliably get hours then? If not, could you get a second job that included Sunday morning hours ('cause unless you're way out in the sticks I bet all the restaurants in your area are packed for Sunday brunch, and somebody's gotta get everything ready for them

)? It's not as good as being up-front with your dad, but if you can't or won't do that, having a Sunday morning job would at least give you a "good excuse," and help you earn money to become more independent.
You don't say what you do believe, but if there's any place of worship in your area that's relatively compatible with those beliefs, could you join that congregation without it becoming a huge issue with your father?