As with many things in the working world, it depends on when your manager says you should clock in above all, and then what the company policy says.
Commute Time and Pay
Let's say I'm working hourly at office in A-Town. The company's lease is going to expire and they decide to move the office to B-Town. A-Town was a 15 minute commute for me. B-Town is a 45 minute commute. Do I get to bill the company for the additional 60 minutes a day I spend commuting because of the change?
Think of the commuting situation as a 'perk'. Part of the cost-benefit analysis you do for any job should be how long it actually takes you to get to your desk. This is a great question to ask in interviews before you decide to take the job as it can greatly change how you value the job offer.
Negotiating Poor Conditions
When you have poor commuting conditions, the best you can hope for is to negotiate better pay to make up for the poor commuting conditions, or some other perk to mitigate that drawback.
Is your issue that you hate waiting for the shuttle? Then try to negotiate a parking space in the main lot. Do you care more about the potential 20 minutes you may wait for the shuttle? Adjust your hourly rate so that for 480 minutes (8 hours) in the office, you are getting paid for 520 minutes (including the shuttle time).
If you are on a contract with regular renewal, this may be difficult to negotiate mid-stream, but is something to consider moving forward or the next time you get a job with similar conditions.
Talk to your Manager
If you are not at a point where you can negotiate, I suggest you talk with your manager. If your company is not recording your time automatically (punch cards, computer on-off time, badged in/out of the front door, etc.), then the final say over how your time gets logged will likely fall to your manager. Even if the official rule is, "Only log time that the employee is at their workstation" or something of the sort, your manager may be able to grease the wheels of justice to something more amenable to you.
Hey boss, I've always been clocking my time from the time I get to my desk until the time I leave it. Since I park in the satellite lot, and am at the mercy of the shuttle as to when I show up. Even though I get my work done by the end of the day, because of that shuttle I have to stick around another 15-30 minutes to get the same pay because of the shuttle. Any chance you would be okay with me rounding up my time worked so long as I get the job done?
Assuming everything you say is true, and you've been doing a good job, your boss may be more interested in keeping you happy than in enforcing the letter of the law. At the end of the day though, you should go by whatever he says, which means living at the mercy of the shuttle if he says it's necessary until you have a chance to negotiate the terms of your employment.