This is never a deal I would take, even as a junior developer not making six figures.
In the unlikely event that your equity is EVER worth anything, the difference between 0.1% and 1% and 10% is the difference between you being super-rich, or super-duper-rich, or super-duper-mega-rich. Not a meaningful difference for many, as far as the incentive structures go.
Keeping the slices small allows the company to scale out and make sure that dozens or hundreds of its early employees will become very wealthy when the IPO happens. In many people's eyes, this is better than having a smaller early team get even richer. If the first 100 people all get 0.1%, you've only given out a total of 10% of the company, but every single one of those people are gonna be ridiculously wealthy in an IPO, and so you can motivate an entire early team that way...and increase your overall likelihood of hitting that payoff some day.
Only if you're a financial moron. Even "IPO" doesn't mean Facebook money 99.9% of the time. If you're fantastically lucky, and the company you work for pulls of a $100M IPO, the difference between 0.1% and 1% is the difference between $100,000 (a nice bonus) and $1M (a nice nest egg). And that's if it's not been diluted (and it will be).
More likely, your company will fail (you get nothing) or get acquihired for $10M cash, at which point the difference between 0.1% and 1% is the difference after vesting between $10,000 ("yikes, will I even have anything after taxes?") and $100,000 (a nice bonus).
Seriously, if you're a developer thinking about working for a start-up, do yourself a favor and take half an hour to read the following two articles:
1. http://rob.by/2013/negotiating-your-startup-job-offer/
2. https://michaelochurch.wordpress.com/2013/06/23/heres-the-pr...
If you took 10m of funding and exited for 100m your VCs will NOT be happy, they need you to hit it out of the park to balance out all the losers in their portfolio. Similarly, your engineers who are taking less-than-competitive wages should not be happy, your founders should not be happy. Everybody's interests should be aligned, and focused on getting spectacular returns, not simply good ones.
We're saying the same thing. It's either worth a TON of money, in very very rare cases, or it's really not worth considering as part of your compensation package. Getting even a 6-figure cashout after taking a 5-figure paycut for 10 years isn't necessarily even a break-even for you. You might have LOST money on that deal. As such, the equity is NOT there (and shouldn't be interpreted) as a cash-like form of compensation. It is not that. It is motivation for you to get the company to Facebook status. That's all it is. So, back to OP's question: why give so little? Because if the company gave you more, you would be tempted to build a 100m company, and that's just not gonna cut it. Instead, many companies would rather motivate a larger group of people to want it to be a Facebook-level enterprise someday.
The opportunity cost of the 0.1% should be seen relative to things like a controlling 30% at a $5 million exit and similar exits unattractive to VC.
There seems to be a fallacious premise that the size of an equity grant is inversely proportional to the odds of a massive exit.
That's a tough pill to swallow but it's a good thing you realized it and are doing so now, rather than after you took the job as first engineer. Your insight is 100% correct. You, as the first engineer, are taking on a huge amount of the risk of the startup and the work but you aren't getting the upside like the founders are.
Instead I took my normal hourly rate and told the owners they could, if they felt generous, thank me if they ever became financially successful. This worked well because I felt I was being paid fairly and they felt I was not taking advantage of the company. It was less risky on my part, of course, because I was being paid for my work. When they sold the company they did thank me generously. I was probably one of the happiest people involved. I didn't have to fight for my equity to be meaningful and I could just focus on my job and the business needs all the way through the acquisition. It was a win win all around.