Gina,
You asked a VERY good question up there - I hope you don't mind if I reply.
Yes, it is perfectly normal to go through stages of doubting - and what Blue Impulse said was pretty cluey... pay close attention to her post!
I think what comes up then is the SEVERITY of your doubts - there's the normal '*** I'm thinking about spending the REST OF MY LIFE with ONE MAN' kinda doubts, and then there are the ones where you start seeing character flaws. They're the ones you really have to pay attention to, and work out whether you can live with them for 50/60 years, even more.
I know a bit of your story now, so I hope you can bear with me with this next part.
First things I would look at with your doubts:
1) Is it because he is an unbeliever? Then I think you are pretty wise to have doubts. If you have a look at most of the posts put by women married to unbelieving spouses, you will begin to understand what a rough trot it is. It's pretty simple to say 'oh yes hon, raise our family in a Christian home' when you're just considering marriage, but it's a whole other ball game once you're there. This requires you being specific in what you mean by a 'Christian Home'. If that means all of you attend church together every Sunday - then make it clear. If that means saying grace at every meal - then make it clear. If that means you want to dedicate your child in your denomination, promising for both parents to raise this baby in the Christian faith - then make it clear. I can't stress enough how important it is to be GRAPHIC in explaining what you mean by a 'Christian Home', and sharing with your bf how important your faith is to you. If you are with an unbeliever, as hard as it is, there will be times where you will feel 'pulled' from your husband, because of what God is leading you to. It's tough to say this, but it's true. If you're a Christian, God HAS to come first - above ANYONE else - and a non-Christian spouse will be VERY hurt by this, and will come to resent you for it at one time or another. That's when you have to make a decision as to whether you want to make your husband happy or God - that's VERY blunt, but it's true - and most women in here with an unsaved spouse can share with you how hard it is when you can't keep both God and your husband happy at the same time - and they've often had to disappoint one of them for the other - causing much division in the relationship. With this, you have to be a witness of a Christian woman to your husband - if he thinks you're 'wishy washy' with your faith, then it will not encourage him to get closer to God - in fact it will probably draw him more away. That's when you need to pray, that if you choose to marry an unbeliever, that you will continue to be a witness of Jesus Christ, at all times - even when it's impossibly hard.
2) Is it about the way finances are handled? This is also a serious topic. As much as it is hard to understand, you will have time off from work if or when you have children - can you trust your husband to provide for you EVERY week at a STABLE amount? Same with his spending - does he often let bills/utilities slide to ensure he can spend his money on entertainment? Does he save well? Do you have a good 'rainy day fund' that does not get touched, unless of DIRE emergency (ie dead car, penniless in another country, etc). Finances are a HUGE thing when it comes to a relationship/marriage - it is the cause of a lot of fights, when one person doesn't think the other is behaving wisely when it comes to their money. One of my big things in a relationship was to ensure my boyfriend had a steady, regular income (that wasn't fluctuating from week to week - ie I wasn't comfortable with 'commission only' jobs or 'temp' jobs - I wanted security in my home), and that even if he did seem to spend a bit on entertainment, he was still saving a fair bit from his paycheck every fortnight. B does - he may spend about $150 in entertainment a fortnight, but he saved over twice that, and was also putting quite a bit on his credit card. So long as he was saving more than he was spending in entertainment/frivolous things, I could deal with the influx of DVDs and PS2 games.
3) Is it just a difference in interest? That is pretty much a no-brainer - you can't expect him to enjoy the same things as you. For example, I like watching Sex and The City - B likes watch Babylon 5. Both of us can't stand what the other watches - and gets frustrated when the person spends all day watching those DVDs. So, we have a compromise now - if we are both at home, it's fine for one to be on the computer doing what they like, whilst the other watches the DVD. At some point though, if one of us wants to go out, then the other should go with them and keep them company. We usually at night have an agreement where B gets 1-2 hours alone on the computer to 'wind down', and then we spend time together after that. All that requires is an ability on both parts to compromise.
There are things like belief structures in both of you that are harder to work on. This is where most trouble starts between couples - even between Christian couples. I know, because this was the problem with my ex and I, and it became almost insurmountable for either of us to compromise to what the other wanted. It ended up in very unhealthy behaviour patterns, so it was wiser to split up at the end than to continue. Have a look at your boundaries - if you put a boundary up (not just physical, but could be something like 'I do not appreciate it when you use those words in an argument, please don't), how does he respond? If you are continually seeing boundaries you want in place in your relationship being pulled down by him - or him trying to coerce you to let them lax - then you have a big problem with disrepectfulness, and that should never be allowed to continue. It would be big red flags for me, and I would seriously consider walking away.
I'm sorry for the huge diatribe up there, but I hope you understand where I'm coming from. I was just trying to highlight some of the major issues that cause deep division in relationships, and how doubts creeping in in regards to these areas are serious ones, and should not be simply glossed over as 'cold feet'.
Oh yeah, and Gina, if I may, I would STRONGLY encourage you to read Boundaries in Dating (Henry Cloud and John Townsend) - it is the best book I've read about how to maintain respect and healthy attitudes in dating (and no it's not all about sex - it's also about honesty, treating each other right, and how to have healthy disagreements, and what you can and can't put up with in a relationship). It would be my highest recommendation for you right now.
Also - have a chat to Starelda, or Blue Impulse or Jenna - young women whose husbands aren't walking right with the Lord (I'm sure they won't mind me advising you this way) - they are pretty forthright when it comes to explaining the issues they had with an unbelieving spouse...

Keep praying - I will stay in prayer with you! It's a REALLY tough spot to be in, when you find yourself in doubt...
Love Sasch