Ftyjtk

In startups, but not only in startup, employees can have perks, e.g. travel in "economy plus", or flexible hours, which are not documented in the employment contract.
The perks I am referring to have been around the company for years and are expected by employees.
If a manager takes such established perks away from a single employee, but not from others, is the employee entitled to have equal treatment to (at least) employees in the same role?

In my case, I am not not allowed to get extra legroom anymore on flights. Without it, I can't physically sit down.

There are too many unknowns here to answer what amounts to a legal question definitively (jurisdiction, contract terms etc.)

However, there are other things you can do - none of which are consequence-free, which should be borne in mind.

First off, soft power is probably the best way to get this done. If you know a reasonable person in a position of authority with enough power to have this change made, bring your complaint to them, if you think this has any chance of succeeding. (It's hard to judge if this is sensible for someone who does not know your workplace as you do, so decide for yourself if this is wise.)

In any case, document your grievance and your attempts to have it resolved throughout.

Keep a diary for this, logging relevant events, use email in preference to phone calls or meetings (but log phone calls and conversations after they happen, along with a memo of what transpired), complain about it in emails when flights are being booked, specifically mention your height, keep hardcopies of your emails and the responses, take photos that illustrate how bad things are for you in flights, and send them on to the relevant people and/or your superiors. Take note of the airline, flight numbers and seat numbers, as well as the specific airplane model you're flying on, and keep ticket stubs for good measure.

If you can, get a doctor to weigh in: this is easily enough done. I imagine you're in quite a bit of physical distress after a flight, so go and see a doctor and get treatment for it, even if it's just a mild painkiller, sleeping tablets or something to relieve muscle stiffness. (You don't even have to take them.) For a small fee, the doctor will write up a to-whom-it-may-concern document along the lines of a sick note that you can put in your dossier.

If this sounds like you're preparing a suit, that's because in essence you are: you're collecting evidence of a reasonable grievance to present, though not necessarily to a court. After a couple of flights, you should have enough documentation to win anyone over. A savvy manager or HR person should recognize from the get-go that your grievance is a very real one, and that this is potentially bad news for the company as well as for your knees, and they will make the necessary changes to policy.

With luck, you'll never have to pull the trigger on a legal action that you don't want to take in the first instance, and your lawyer will be delighted with how well you've prepared things for them if this continues to be a matter of contention.

And if you do want definitive legal advice as to your rights as an employee in this regard in your jurisdiction, if it's an option where you are, join a union, if you're not already a member; this is probably the single simplest thing you can do to move forward on this. Legal advice services usually come with membership, and you'll end up paying a lot less in your annual dues than you would to a lawyer for a one-off consultation. They may also be highly effective intermediaries in pressuring the company to make proper allowance for your physical size.

As I said, none of these actions are consequence-free (except, perhaps, getting advice from a union's legal services, in and of itself). Unfortunately it seems you'll have to stand up for yourself to get what anyone should be able to see is (literally) reasonable accommodation for your height.