It means that the base salary is taxed at normal rates, but only 50% of the flight allowances accounts toward the taxable income, and toward the social security/pension. The other 50% is tax free.
To make it quick:
All your base salary plus half of your flight allowances (flight pay, or whatever is dependant on the flight activity) constitutes your taxable income. Per diems are of course tax free.
On that you pay about 12% of social security/pension, from your payslip. The employer pays about 25%.
On the above taxable income, minus your share of social security you pay taxes, with these rates:
23% up to 15000
27% from 15000 to 28000
38% from 28000 to 55000
41% from 55000 to 75000
43% over 75000
Deductions are present for wife, children, mortages, medical expenses, voluntary contributions to private pension funds, and some other stuff.
The total taxation can be somehow reasonable, especially if you have a low base salary and and high flight allowances, like most of the italian airlines do.