SPSGirl - I'm really sorry you had this experience, we had something similar so I thought I'd share.
My (very traditional/catholic CofE) church is welcoming of children however, there are the 'few' who don't like the noise etc. DS2 (aged 18 months) decided to do a runner to the front of church, DH stupidly trusted that DS2 would stop
. Before that, he'd been good at walking around at the back of church but, I know my parents would have told me if they could hear him. Anyhow, churchwarden told me after that people were finding him distracting and he was making too much noise. I replied that I was glad we went to such a child friendly church and then cried all the way home when no-one from church could see.
DH emailed both churchwardens and PCC chair (no Vicar at that point) asking that we did something for small children. Nice churchwarden and PCC chair both replied saying they were open to ideas/improvements and that they were upset that I'd been upset (we knew the nasty churchwarden wouldn't have mentioned it to them). From then on, small children were welcome to go to Sunday School and run around/make noise. We also have a crèche which a year later (mainly due to new Vicar, his wife and I having a 'moment') has been updated for the first time in 40 years. The crèche thing caused conversation in PCC with someone arguing what would we do if it brought lots of noisy children into church-Vicar replied that he'd still say Mass, just a bit louder
. Still only two people that I know of who find it a problem and a lot of other (less grumbly hence quieter) people who love my crazy child and remind me how much he takes after me (apparently I was known as Little Miss Wrigglebottom for a while...).
Please don't give up for the sake of a few grumbly people who need to be shaken up and made to question/remember why they go to church. I know it makes you feel paranoid of every cough/giggle they make but that feeling goes. Speak to your Vicar, speak to the churchwardens, explain you want to keep coming but it is difficult if you know 'other people' find them distracting. Ask for their advice and prayer. It could be there is someone sitting quietly who has been waiting for the opportunity to do something for your children.
(As an aside I should probably say that DH is going to train to be a priest soon so does a little preaching at our church. Preached on the importance of children in church just after the incident. Also, as 'Vicar's Wife' I am going to make sure my children are the noisiest so that no-one else feels bad. 