EULAs are pretty long and confusing, but you should read what the font EULA says. Do you plan to keep the font or give it to the client? You are most likely not allowed to do both per the EULA, and if you send it to the printer with the ID files, they should probably own their own copy too (not to worry about that last bit so much, as most printers are using a PDF workflow now days).
In other industries, like auto repair, a shop will buy parts and charge you for them at a higher price than they pay, but that may or may not be what freelance designers do (I've never done it, but I have done very little freelance work).
I don't think the question is should the font file itself be passed on, but should the cost of acquiring it be.
I'm probably NOT the typical freelancer, but this is how I would handle it...
Include a charge for the font (at cost) on the invoice for the job if this is not fairly common font that you just don't happen to have yet, so the client knows you had to spend money to complete the work, then, if this is a generally useful font that you might use again for some other work, discount the entire amount (you don't charge clients for your other fonts, do you?).
If the font will likely never be used for anyone but this client, you have three options, based on how good the client is likely to be for your business:
1) Discount the entire cost on the first bill as a show of good faith, especially if the remainder of the project billing will cover the cost of the font, or it's an established client.
2) Discount a portion of the cost on each of several bills, perhaps the first three, as they continue to do business with you. (Worst case here is you eat the first installment discount if you never see the cleint again, but you win some points for being willing to invest in your tools, even if not really useful)
3) Bill the entire cost without a discount.
I would use this last option only for a large company with a big budget that expects to pay for that sort of thing, or if you have discussed the necessity of purchasing a specialized font with the client in advance. Most of my clients are very small companies, individuals or non-profits with small budgets and I wouldn't dream of sticking them with charges for a few hundred dollars for a font I could use again. This actually happened to me last year, with one of my non-profits, and I ate the cost of a font to re-build their logo ($170) even though even they use it no other way. Billing for the labor was $187.50, so I ended up making a very small amount of money for the three hours I put into the job, including the time it took to identify the font, but they continue to send me work once or twice a year that pays very well.
Thanks, Peter. That sounds like a reasonable way of sorting it out.